[English] 日本語
Yorodumi
- PDB-6vme: Human ESCRT-I heterotetramer headpiece -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vme
TitleHuman ESCRT-I heterotetramer headpiece
Components
  • Multivesicular body subunit 12A
  • Tumor susceptibility gene 101 protein
  • Vacuolar protein sorting-associated protein 28 homolog
  • Vacuolar protein sorting-associated protein 37B
KeywordsPROTEIN TRANSPORT / Endosomal transport / HIV release / macroautophagy
Function / homology
Function and homology information


virus maturation / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / regulation of epidermal growth factor receptor signaling pathway / viral budding / regulation of MAP kinase activity ...virus maturation / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / regulation of epidermal growth factor receptor signaling pathway / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / receptor catabolic process / positive regulation of exosomal secretion / protein targeting to vacuole / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endosome to lysosome transport via multivesicular body sorting pathway / Flemming body / virion binding / protein targeting to membrane / endosome to lysosome transport / viral budding via host ESCRT complex / negative regulation of epidermal growth factor receptor signaling pathway / viral release from host cell / autophagosome maturation / keratinocyte differentiation / multivesicular body / negative regulation of protein ubiquitination / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / ubiquitin binding / HCMV Late Events / macroautophagy / regulation of cell growth / Late endosomal microautophagy / Budding and maturation of HIV virion / SH3 domain binding / protein modification process / positive regulation of protein catabolic process / calcium-dependent protein binding / late endosome membrane / transcription corepressor activity / late endosome / midbody / early endosome membrane / vesicle / early endosome / regulation of cell cycle / endosome membrane / endosome / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / lipid binding / ubiquitin protein ligase binding / centrosome / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Multivesicular body subunit 12A / Multivesicular body subunit 12 / Multivesicular body subunit 12 / Helix Hairpins - #820 / Modifier of rudimentary, Modr / UMA domain / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / UMA domain profile. / Vacuolar protein sorting-associated Vps28 ...Multivesicular body subunit 12A / Multivesicular body subunit 12 / Multivesicular body subunit 12 / Helix Hairpins - #820 / Modifier of rudimentary, Modr / UMA domain / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / UMA domain profile. / Vacuolar protein sorting-associated Vps28 / Vacuolar protein sorting-associated, VPS28, N-terminal / Vacuolar protein sorting-associated, VPS28, C-terminal / MABP domain / VPS28, C-terminal domain superfamily / VPS28, N-terminal domain superfamily / VPS28 protein / VPS28 C-terminal domain profile. / VPS28 N-terminal domain profile. / MABP domain profile. / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / Helix hairpin bin domain superfamily / Helix Hairpins / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Helix non-globular / Special
Similarity search - Domain/homology
Multivesicular body subunit 12A / Tumor susceptibility gene 101 protein / Vacuolar protein sorting-associated protein 37B / Vacuolar protein sorting-associated protein 28 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsFlower, T.G. / Hurley, J.H. / Tjahjono, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI112442 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission.
Authors: Flower, T.G. / Takahashi, Y. / Hudait, A. / Rose, K. / Tjahjono, N. / Pak, A.J. / Yokom, A.L. / Liang, X. / Wang, H.G. / Bouamr, F. / Voth, G.A. / Hurley, J.H.
History
DepositionJan 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Tumor susceptibility gene 101 protein
C: Vacuolar protein sorting-associated protein 37B
D: Multivesicular body subunit 12A
E: Vacuolar protein sorting-associated protein 28 homolog
F: Tumor susceptibility gene 101 protein
G: Tumor susceptibility gene 101 protein
H: Tumor susceptibility gene 101 protein
I: Tumor susceptibility gene 101 protein
J: Tumor susceptibility gene 101 protein
K: Vacuolar protein sorting-associated protein 37B
L: Vacuolar protein sorting-associated protein 37B
M: Vacuolar protein sorting-associated protein 37B
N: Vacuolar protein sorting-associated protein 37B
O: Vacuolar protein sorting-associated protein 37B
P: Multivesicular body subunit 12A
Q: Multivesicular body subunit 12A
R: Multivesicular body subunit 12A
A: Multivesicular body subunit 12A
T: Multivesicular body subunit 12A
U: Vacuolar protein sorting-associated protein 28 homolog
V: Vacuolar protein sorting-associated protein 28 homolog
W: Vacuolar protein sorting-associated protein 28 homolog
X: Vacuolar protein sorting-associated protein 28 homolog
Y: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)204,22224
Polymers204,22224
Non-polymers00
Water5,549308
1
B: Tumor susceptibility gene 101 protein
C: Vacuolar protein sorting-associated protein 37B
D: Multivesicular body subunit 12A
E: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers34,0374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-52 kcal/mol
Surface area13360 Å2
MethodPISA
2
F: Tumor susceptibility gene 101 protein
K: Vacuolar protein sorting-associated protein 37B
P: Multivesicular body subunit 12A
U: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers34,0374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-53 kcal/mol
Surface area13430 Å2
MethodPISA
3
G: Tumor susceptibility gene 101 protein
L: Vacuolar protein sorting-associated protein 37B
Q: Multivesicular body subunit 12A
V: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers34,0374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-51 kcal/mol
Surface area13050 Å2
MethodPISA
4
H: Tumor susceptibility gene 101 protein
M: Vacuolar protein sorting-associated protein 37B
R: Multivesicular body subunit 12A
W: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers34,0374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-56 kcal/mol
Surface area13510 Å2
MethodPISA
5
I: Tumor susceptibility gene 101 protein
N: Vacuolar protein sorting-associated protein 37B
A: Multivesicular body subunit 12A
X: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers34,0374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-52 kcal/mol
Surface area13240 Å2
MethodPISA
6
J: Tumor susceptibility gene 101 protein
O: Vacuolar protein sorting-associated protein 37B
T: Multivesicular body subunit 12A
Y: Vacuolar protein sorting-associated protein 28 homolog


Theoretical massNumber of molelcules
Total (without water)34,0374
Polymers34,0374
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-53 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.584, 162.584, 139.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein
Tumor susceptibility gene 101 protein / ESCRT-I complex subunit TSG101


Mass: 9343.720 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q99816
#2: Protein
Vacuolar protein sorting-associated protein 37B / hVps37B / ESCRT-I complex subunit VPS37B


Mass: 8061.243 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS37B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9H9H4
#3: Protein/peptide
Multivesicular body subunit 12A / CIN85/CD2AP family-binding protein / ESCRT-I complex subunit MVB12A / Protein FAM125A


Mass: 2655.937 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVB12A, CFBP, FAM125A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96EY5
#4: Protein
Vacuolar protein sorting-associated protein 28 homolog / H-Vps28 / ESCRT-I complex subunit VPS28


Mass: 13976.124 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UK41
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2 % w/v gamma-Polyglutamic acid (gamma-PGA), 100 mM sodium formate, 100 mM sodium acetate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.19→99.18 Å / Num. obs: 107460 / % possible obs: 99.46 % / Redundancy: 20 % / Biso Wilson estimate: 48.48 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.04189 / Net I/σ(I): 17.22
Reflection shellResolution: 2.19→2.269 Å / Num. unique obs: 10167 / CC1/2: 0.281 / % possible all: 95.09

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.17_3644refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F66

2f66


Resolution: 2.19→99.18 Å / SU ML: 0.2757 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3667
RfactorNum. reflection% reflection
Rfree0.2396 1998 1.87 %
Rwork0.1934 --
obs0.1943 106911 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.12 Å2
Refinement stepCycle: LAST / Resolution: 2.19→99.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12478 0 0 308 12786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812642
X-RAY DIFFRACTIONf_angle_d0.885116991
X-RAY DIFFRACTIONf_chiral_restr0.04511955
X-RAY DIFFRACTIONf_plane_restr0.00562165
X-RAY DIFFRACTIONf_dihedral_angle_d9.89821716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.34361300.29866728X-RAY DIFFRACTION89.47
2.24-2.30.3121390.28257477X-RAY DIFFRACTION99.36
2.3-2.370.33121390.27367516X-RAY DIFFRACTION99.84
2.37-2.450.31621470.25487548X-RAY DIFFRACTION99.94
2.45-2.540.29661400.24137536X-RAY DIFFRACTION99.97
2.54-2.640.29691440.22797520X-RAY DIFFRACTION99.96
2.64-2.760.27531460.21227584X-RAY DIFFRACTION99.96
2.76-2.90.25031430.20027538X-RAY DIFFRACTION100
2.9-3.080.26261380.18777515X-RAY DIFFRACTION100
3.08-3.320.25091430.1897553X-RAY DIFFRACTION99.97
3.32-3.660.22181440.16597563X-RAY DIFFRACTION99.97
3.66-4.190.21621470.16477581X-RAY DIFFRACTION99.97
4.19-5.270.19081460.16577580X-RAY DIFFRACTION99.99
5.27-99.180.23721520.20267674X-RAY DIFFRACTION99.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.471015818462-0.1332788381050.9426419775930.07687034464070.2075949116190.147959396135-0.181564173603-0.2084759015450.0470232648188-0.01852461175460.1296836396870.207692788528-0.0561068349767-0.213311344629.1658517776E-50.426404892817-0.0532722653796-0.01900014205830.3846933935160.006516678134080.38100618821333.8750775394-35.211458904424.1693073293
20.3520455701620.106938284210.4742312168430.924354220561-0.1417093719430.609302821244-0.257153975993-0.5909008328860.603609123053-0.05599066730630.04524596426430.216167634065-0.1177408660340.01887434938060.0002389508477610.441945825251-0.0268454805122-0.04736533997810.3761403967350.03072420429030.47319991977924.6384643109-29.012752981222.1049242688
30.04610996433350.00473943962581-0.1476893096150.331478803132-0.1563006469190.364449438148-0.30467389407-0.1383241356070.0170391508654-0.8642489474970.335070850287-0.27473815129-0.1488091985830.161775154138-0.0004830015486250.480548059634-0.06821203506950.04328966825290.4755296893590.03804427646840.45819744819341.8727322969-34.09063707114.5883616822
40.2754293949880.1020282402770.06829084363220.03955156805740.07298899288030.09169685358810.8860873744971.17458837096-1.574322049450.328924114584-0.3816022195540.4386439206970.8695775569650.0447319014139-0.008729391026370.529998113046-0.0355959241184-0.04812273235480.550681016056-0.04720015229920.56564706404435.723911424-42.197142769117.002866882
50.277403066079-0.1751783752620.02033866964510.11236542761-0.0176864912922-0.0468117002813-0.06770535949540.198456043538-0.06871899012670.113824350547-0.1932397175440.6456517977370.02928760939450.3444730927730.0006136089374820.537293551087-0.0360325316867-0.09991123041980.5129441068790.02607719057040.38305327885523.6606269002-30.101132246412.9498541313
60.2013309164250.134119610922-0.5311114273350.101106787116-0.3627480111551.31957366071.843744471-0.5019115384460.1609952837860.861328391263-0.000125670446846-0.3990470582520.195634435037-1.211691635180.0637171418140.812845977801-0.030241257038-0.3341406212310.6359260447890.1759610842351.7590437760782.5820554569-13.21465774997.98132116356
70.5987463098730.837215458099-1.39023688711.15404808496-1.870818296383.18403517834-0.8835668993260.2104607971990.448924414503-0.8487369872511.0364279301-0.4826951580650.6461599100320.1940195131530.1091443126290.328168804760.1884579044430.005196292416080.562395148424-0.2700202286330.87272884636669.6671207029-12.79957222641.41108396535
80.8741810897430.1115107755710.6694207437580.638465336809-0.7078102036991.141904092590.168924186714-0.0239773795257-0.2909263884560.0536721158453-0.09483955701060.075322597340.133808136946-0.1324625566583.51019886717E-50.4192680120480.0353677789086-0.01160315497460.416711536037-0.02861939804990.38514369761649.5663856111-3.414264054595.22432001317
91.142736673361.34267543850.2988162175741.516667627470.7204076442060.522683050107-0.1119904463280.1209884882210.13719862215-0.097801328528-0.0124906912620.8625752319960.1526386854880.05147802411216.41108891119E-60.4721792585650.000920679832161-0.08940472671810.525639228863-0.1061210396340.49473755026138.82974538121.177175267665.02543097684
100.08987254181-0.0207098946485-0.02694901408380.0337525039119-0.1042049527910.281134667517-0.739123427337-0.705797173801-1.100808057031.14201280326-0.2094397286940.4271260499450.8227581395081.41957742754-0.00127142225740.633515902137-0.0732719777487-0.02803373184530.5526757384570.1336025526960.58043188246449.8632681151-14.808747243214.4171311182
112.945545433751.897145386720.7886315797751.299951013010.5288974431460.238664574835-0.71456017846-2.211222670460.4398662059060.931212843617-0.1799159300650.1744374413642.139514574070.853371193908-0.1146436734560.712665251387-0.01109572189670.034814737750.6938266317580.0139862989380.3545199540852.364902042-6.1975208293916.1101207881
120.139805308501-0.00773391213839-0.01161610039010.0575274087719-0.06379899489120.1941867521240.0248738937948-0.07846426406030.57374731337-0.4275113931770.110024485185-0.762534904238-0.107270730026-0.7026809696770.0001491695985940.6523418322860.065462548088-0.05837356651710.492582642205-0.04567950132550.52126541143854.3714593835-0.22235070591713.8723001155
130.18300980054-0.09255728023090.1131510647790.06013820573590.03704523625330.5688826661490.207994346042-0.5727083140741.218334808610.457572717549-0.8265574534070.9522198884230.28892099496-0.00393082525129-0.01516514502260.526376880051-0.02338061347150.05993973228530.412801890827-0.2195272007650.61309071136437.47865138652.6251498605713.9346514513
140.1555995393150.05771317029080.04248939973070.2022491304310.3693829639380.484013023277-0.6070730751720.3469050503990.2995375240410.800307017959-0.234161978496-0.901546767238-0.4024067850640.8781105821440.0003834906877460.6167440610480.0606166080645-0.1080846955830.5636538603960.07339170707720.74519458875567.9134452375-24.206557903288.5267371242
150.4136609279810.1582655098230.1572776855040.3575278581980.04870421517750.454030684240.179862537405-0.1986636993640.3522183153790.415411442069-0.1116024603820.02426365926640.243736064936-0.0441309843345-4.62425811797E-50.520346947164-0.00347400805998-0.05718219054460.347630152358-0.01793637313380.34245338124944.940075306-19.972651962680.8348228843
160.658100773726-0.4995948669990.2792139255191.60505152953-1.767760211381.81915506872-0.122576466831-0.06658565662890.4385901104210.0770374778290.09415542167990.612728459549-0.102474496394-0.2235146780920.0007146727207040.4318198811470.0318606060597-0.02372633797790.414366054391-0.06275854018810.39793559411634.2043082711-17.358940323278.4617078318
170.903534015409-0.84041735363-0.247522396980.732713459090.3439226937140.1954243554760.03438272135740.4964235280990.0954674812288-0.637266465671-0.350167946996-0.1716292978960.227005506496-0.06389722247590.0001776549751880.494667045269-0.0661269562814-0.005947334616920.4487445086570.03821347457260.42883835071751.6315121174-19.092567932472.1279819033
180.0910034748658-0.0538759264509-0.01530194531630.1470700934470.08972177086160.0168703144861-0.04626006936160.6700728127540.0538201379353-1.589283503860.411373580490.53493831985-0.216662568513-0.963469488591-1.49670221041E-50.582747675384-0.0255167141465-0.09362101140680.473824114367-0.03042809015180.33853912058637.3259715947-20.448102645668.6307320658
190.0109814189059-0.154256292950.009021245049611.742551170730.0132770974494-0.0027956941034-0.5134250925980.8849462052970.876329741404-0.312578870469-0.1401269803040.3719119387180.2373975131690.305748592922-0.006797642777620.631948732524-0.0907820524012-0.1691082300880.7134517184780.1662054727510.60304208108128.9683165469-16.866615744370.2557770002
204.929149781760.55528990228-3.0067478422.93165234648-1.765208141474.466888345490.767684210987-1.16145523320.1132838301241.49478146210.0822797467936-0.4545959182340.2065991105650.7204449400381.570888977430.4886111337010.2452864413-0.483049541634-0.2078245630850.4255569892991.0811551553846.2811405139-54.585750485377.1663554121
210.3363586183360.5879054928050.7093527181911.005857737140.641258443488-0.355601131181-0.25518697211-0.242508476444-0.0671513073826-0.1322728125950.202707933409-0.115608421352-0.0646967060016-0.00014093769324-0.0001211354226610.478130697156-0.0739440410266-0.03575455686610.4667641469870.02509280400060.3663774467629.4313437405-39.827304035169.5324291131
220.3898019695250.422327912168-0.6107932552170.7553974976380.2356375821331.30050033626-0.216186315395-0.01721321662230.2708307302020.08893618191010.0139265057790.294878558657-0.143477279713-0.2130706442832.71556353741E-50.5104666665610.00479294670517-0.01647490352240.453492448499-0.03575012129270.47089408472320.7841118241-32.370259190167.0259291729
230.152577990644-0.1888108783950.006964576545440.2117547688660.09458574326920.381773447795-0.204388129617-0.1338578660940.0581665256292-0.6564925939910.33115837437-1.12624206398-0.5901211849140.39631065020.000588567659760.517747849645-0.07576688714190.04421695320430.665961091236-0.05876528225810.52095199865237.4927564981-39.991382258860.0674963102
240.3060176960770.04199863360510.4332051273110.1559879732680.3358404073230.2831094055460.08167980343380.414529625287-0.0449264503434-0.639126116066-0.24370404344-0.05752733780430.02038060395250.006493377391178.6137320432E-50.456812729906-0.0879398343461-0.1163628381970.5430647994980.03669244575350.43476550811522.4341050957-37.110383234158.8603261771
250.2085816242130.146423661217-0.02855952177040.204326993920.1860267369330.349105051371-0.4436540538310.3042706742270.0192446008828-0.9639758253990.303178587365-0.761463291946-0.3154260359790.029981213976-0.002660563977730.5657033811610.02997510052780.006186597652140.4491465658110.1794734575570.94726783514273.9957766031-35.3000223914-11.1424332917
261.245447131260.813897082228-0.1808332128820.9906974400190.4263729004310.441106859377-0.160924956226-0.1687822511020.1427040332310.1721691098130.158209946748-0.136847120939-0.151160458374-0.07232825341060.0002030288277890.408215033810.04191507435890.02650599315710.3875778435630.01830985518290.35706505196656.0836388642-22.6467203123-9.64913551393
271.057405855730.449035966596-0.7082011689320.697345517354-0.08797520575720.418899521532-0.0940932721308-0.300491750914-0.0508468337487-0.326028623445-0.116739904008-0.2509746139990.154186069213-0.3815468279640.0001930651581850.4676702322970.0188598856853-0.03543354451220.515445892304-0.03976347443680.3798780447148.7232462434-28.9446388422-8.86036737962
280.0612234787412-0.01610776772870.06092521039810.103030883995-0.05423649013980.07291719696840.982397716398-1.09472839503-0.5715427170580.174263851353-0.2753147303830.2377011045520.913121044044-1.43100228576-0.002446914171990.7442087227910.0898102649725-0.2305376490440.8675484324680.181904545460.64215870170659.6940529064-39.99184022913.78967569431
290.521952262264-0.490964176363-0.1719057578430.380103463770.8089284511230.956147797047-0.1839355592190.1234731534261.11409088231-0.148943633439-0.027790855711-0.961804059981-0.5903824033880.1235924197420.001574251819030.509263884175-0.02036863074370.08706316016110.4836274271510.1793008344210.61233798181470.5798621582-17.7210216411-13.7783375583
301.11710715523-0.587365264032-0.4126814229650.6755361878160.7667393010320.545460470012-0.06615028961810.0553830910119-0.170405832364-0.0291863019131-0.0650469153499-0.0691206071354-0.127879074325-0.0475056610883-0.0002433275898670.3580455443730.0193111905640.02351589235360.473374482415-0.007281994368280.40294523131866.5708788522-24.719191126-10.170297191
310.138994600206-0.01406646706020.1316782274290.0307391710804-0.0503544790090.5073905207970.30394272054-0.241597133444-0.3355356463580.80752261281-0.2372194491230.1092890789910.00715513279415-0.3513431389460.002403862502330.533289788823-0.05512333778070.03287203478620.616590577305-0.02730737628480.60208977212460.5601390798-28.82864671441.54174203637
321.29694726705-0.2300551627180.3129849539351.666631362880.3508381916180.149898488747-0.0388181820076-1.25013224685-1.421891581071.323411815830.3267688024850.4240829342481.06640594410.2232641019530.1749085219850.3001871925040.175294243509-0.1212990160440.4644815889550.04305222914260.73540675939873.5659279796-37.2221384325-4.21249053339
330.319348670293-0.0227111176376-0.3655329905410.08182366401710.04471733080210.2408914639720.443480050931-0.500750502971-0.1965761934120.137589779832-0.3052002420960.3543767151560.468415570055-0.239638125305-0.0003692515571580.5621656912080.0465796026776-0.08932025458830.498103779202-0.06938155998090.83926215942457.0971204837-47.4184426935-8.1646243742
340.2802813883060.6362882333980.02785405699910.951145025979-0.2542390411380.424641194151-0.1770800228530.08083787385920.06250929855750.2256187928410.3713337081950.1457299864510.07141155689380.003449091547350.0002541200379980.3725412764970.04481084283-0.07799433342660.435847888344-0.0308380483310.36281344358241.3300036592-24.1879518955-6.40813664501
352.004432124360.0733520376734-1.151458004310.821271511970.4444410123420.7464506014680.213896775307-0.01022226115710.07992963927060.173867671777-0.3054879947840.3518115115860.04315341789880.0709290161769-0.0002479969679650.500778179050.0146286180428-0.1350386995020.483371616487-0.05989326035530.44696091393333.1465804046-24.9006769505-4.46158994656
360.7965673236360.372691625520.1318981057230.5488314409240.225478300617-0.04812004062060.0729355603588-0.3839368913580.1679531735380.252597545752-0.2991075842980.250112554573-0.0177036238908-0.0284594614046-0.0004882925821020.490327094597-0.00284370381409-0.04342054657550.569651025256-0.1001734521440.446867198138.8987630913-23.17708426093.10396953026
371.105052305380.20794705816-0.5386328989020.739822644076-0.318739207689-0.0601017444128-0.246037646699-0.0520473469995-0.189792477375-0.03240646379870.129880937422-0.1266656350770.15660879301-0.0707430457244.89518931535E-50.413173347183-0.00847640759649-0.01014519618730.373639491153-0.00228347006970.40898904223255.3374980454-29.416212472342.8192847721
380.7331636927010.7275894292310.2269836872721.551766752780.02909549804050.397528935272-0.06359279459780.1846277210740.0439476887699-0.095841374947-0.01612960995260.0859255901655-0.073955818913-0.104792493803-0.0002801853523930.383437902022-0.005054264862820.008907565219210.353681144790.008345481656270.39861965483354.0019177223-18.750264713138.5309581202
391.48736730782-0.311089356971-1.054759703190.7260825519870.5777865573370.5083654478090.179009476798-0.40414104777-0.4211318489380.09609097269820.0001340408723160.1508241761630.0361561037059-0.1563554646750.0004727273947210.386619261593-0.0513527266004-0.04662716640860.3796863011650.0864110780420.40009122939835.4700464695-54.007201062130.1067929244
401.314142682390.7397090737820.792548576130.689128640203-0.4434992593311.11265165213-0.0947422162306-0.2249188524780.2338222805480.03361759985770.0483070956713-0.1220109986360.033981220129-0.0229223163067-0.0003857363711480.417203990735-0.0441088248407-0.06271708971460.332312227704-0.0006889080359670.40473940646334.4944796708-43.015928266227.7715206245
410.6160652176990.5066597214460.2931593465040.4248218025540.3348624140960.6512735328190.0416832195475-0.0465950027789-0.862937765701-0.45498669834-0.2455029018861.12037711293-0.2901497043350.130323620084-0.001273930960820.809956347434-0.2048397873670.09875163511091.308658691870.1708475756860.99949560160181.573330859110.9730772924-2.92416327684
421.187179686570.4357250849870.8187852569480.01318090017140.1956380352080.0994295882162-0.1170036055180.07206904557190.3019575537150.07502692563850.275283199622-0.254234050692-0.4512602096430.2033997967320.000420777132380.405665707204-0.01040480127510.01316165727610.483850133521-0.005531641989580.41732424168865.0041643166.352348558923.28922231553
430.08098717259960.5403293591140.03775324874923.985914927690.3841999222970.0241803255514-0.130238221594-0.07270426552930.422017931219-0.1106106332851.381467453681.68277092464-1.77910026576-0.09583452073020.1595225428240.882622115850.118957975798-0.004378628246670.671013370318-0.1103142950520.7789213357745.730633175217.8222561591-4.00742028271
440.3781543204830.543123016834-0.1637636070881.06527424202-0.2961402884180.1888139788460.189370238803-0.4192369683870.248763606188-0.107891639132-0.138226141623-0.6115064531110.0214900388305-0.1626277957855.97827309137E-50.5015997581980.02468502165460.002230352921530.500440587445-0.07242826094320.40659708699558.3564402298-1.031314974554.06240930183
451.60442170895-1.5445131667-0.6816300378730.66723899512-0.308257543609-0.4417134500510.00657528202936-0.08743110830850.0321210004481-0.0280952127095-0.000666252414409-0.1185994285760.0617890532095-0.08011973273092.53269151515E-50.4424559516630.031048311299-0.02385307524250.405293048767-0.02031802766530.4285257313949.9445313874-36.490949620888.5124600091
461.31646786506-0.06234280049871.161925071460.7665836251120.005439088435080.7793488210240.0852027149177-0.199663385727-0.1851510654790.132618222383-0.0951156167483-0.418836975383-0.169368829858-0.01818572452560.0003224297543470.398002504055-0.00173787423496-0.0128749686110.3375325033890.05744715043590.45126083848450.6088289692-26.306952010484.285800764
471.087806140280.326618489061.106680414710.1061377989980.09838815067040.592513870190.190127435496-0.483837569795-0.4054754016480.1247079471910.0465776963823-0.2996128705630.213564522894-0.282917214736-6.63197156102E-60.535492443565-0.154296117271-0.1102871102960.6025186514340.2114353206810.62760286616625.2782066356-57.325889045875.7646022513
481.294363121190.530174318930.8165818504941.52850337652-0.2102408197530.5206974498150.372826870097-0.696578842196-0.535874570383-0.269435893570.211685956849-0.349767065991-0.1497200565820.144997793629-0.003885383261170.455590471113-0.102761480138-0.1163152483380.4072342916920.07702113648450.46680777752230.9965645398-48.055299138272.4457260077
490.3271220137090.08588278052720.3752990815051.362694546480.9343484831230.640526648450.0563727900592-0.812181249348-1.02652987093-0.1746180246810.1301933299140.1248465482920.219399572573-0.0334729274542-0.0003500140265940.536520670413-0.00250525504577-0.01424511621610.4284794087380.07980692123310.53917537234856.1039281211-42.519658641746.9863704063
501.57733360667-0.1673519386240.9140282992790.6735421838160.6324972093130.773837133254-0.0795835928332-0.371503714694-0.2254668455440.08104526381450.109805394971-0.145417210340.131473152110.213047650669-0.0005461116796340.453305727370.0107304177052-0.05123709184720.3547510211790.01748239104160.46411871364657.1007994736-35.363228247244.7284828415
510.102842430070.275304839641-0.004385995988090.4403194632520.5393900055160.2500964468510.319189061786-0.124377518373-0.800465921897-0.23010726147-0.581947114777-0.09351786860840.057537580826-0.416141578418-0.1301787555870.516030322557-0.08385662302770.02811387326690.4704428492690.2143770453060.86485338091426.8936875122-64.81560710433.9440758824
521.706681051750.2068389874240.6486895790940.4762116599880.03436347206080.000476517930287-0.0415756369075-0.234305005461-0.5683733080780.3446674378090.008080945127740.09761024252030.10166002668-0.06430616539910.02294445278260.493310851077-0.0159310539028-0.06309438144180.3991161128560.0606834185920.55551104088531.6235225955-59.110374681932.0619185202
530.5671934488530.2228023855250.6555600149010.6052454834230.2571760641170.0817974953325-0.09493230786410.3709943297791.24144145052-0.143491064723-0.183170343227-0.121683161554-0.548037608325-0.0479844952879-0.003283999907580.762190031004-0.1313254832080.06612372773010.7355757519150.1544055400250.60715673983271.730473044319.99250811-0.316239597551
540.4169802250460.04505531286260.4441778403111.169899413340.1984713622730.00484020410954-0.05984516364420.557121804427-0.0667773515682-0.257882177059-0.00560150369948-0.257187704938-0.2003060070890.246996973711-0.0004972453446830.605982125836-0.001705942380780.07758527470050.600437166520.04650094933960.43998550964268.603533274812.86437620450.639054307277
550.312768247924-0.2829062110540.1895181070760.6702088699430.912640719630.736289905697-0.290979813777-0.575443917847-1.36554693297-0.02084651337680.3068680528830.8880943938910.214939918761-0.1679145436970.000749520696210.5003617759950.01350976153660.1261246856160.5001782298270.1737872378990.63013146797149.5073121183-50.081726762694.4181289243
560.421687571482-0.3622544235960.4873248807571.59372679678-0.09054066250240.653322056868-0.335847491077-0.20642590540.003622255020010.39795377750.161168067611-0.01183011173910.0590598226525-0.265931151867-0.000621316293460.4678245315230.03359141769790.001892601590610.438578310052-0.001998780592870.34709977820650.0699326268-42.338440657991.5293745927
570.88609769359-0.844696457580.7246565386630.440826862209-0.209540492909-0.120806529984-0.5692258535960.09246255334690.2485898224331.480727373950.594040434659-0.1554919494770.535808012008-1.634936607660.05456159419760.716995139713-0.400761747422-0.1247647857450.6318194001160.2901128588490.83626982727517.2055990502-67.799068566179.0184658966
580.642585264594-1.530766236630.6376891811520.3119263165350.2290402317550.4951971259970.971657550729-1.11810507507-0.6788879934841.08960580271-0.72326347866-0.0487257576976-0.0886692755565-0.2008051097650.1631013600310.705499106217-0.116557060635-0.3231048814670.5506951673860.3533765279080.81943156382822.4074096985-62.217174577877.7400661071
590.167065952723-0.101839211949-0.1265760759950.06990962702850.1125864745480.130160223968-1.037009837871.17799777221-0.537265989428-0.4840150072560.565827000134-0.2995213760250.2747079063760.645743901953-0.001636254034130.495220902403-0.06606191937190.02744357959920.577472974221-0.09416828633430.51908785584360.4938387454-29.472770242131.9886597834
600.323867096353-0.8833453702270.05938080439783.10127198998-0.5672268555710.1217444228030.435535399715-0.1967119179140.677793734386-0.869313984643-0.278791060792-0.1724180067080.5853216899120.5716795044560.1831597896790.242622479981-0.0842724293028-0.1298633218890.844755249436-0.01596278501870.58469808055974.4179964323-33.790350206642.1624219249
614.95948323678-2.719954813510.8801116609072.001425597241.616370755066.98593654906-0.3711538721820.2037881582270.6923409037040.681978781585-2.422956286490.00945112485181-0.218571412496-1.03509438258-1.693748194350.3502152179030.324665483625-0.2889420777480.818574627725-0.3828446025390.57177763595338.470036553-55.166195235520.2535351305
620.545945643937-0.175470952429-0.2085381185620.2096380729940.04331510023840.184719649926-0.5318605084060.974319218334-0.914296173069-0.199951906324-0.222202088362-0.3857145036950.427070881756-0.2006653259820.00999889413220.4623370736210.0945377226332-0.008948874342340.7019183186650.0404579866610.85259460130746.8929025819-65.280838547427.0932120041
630.0617494941630.008418516773630.03426070305610.191759893610.144295057850.229693213123-0.507445448122-0.8333978065610.0614146866050.299119034430.4993726293840.06548199450660.650438876213-0.0338528850541-0.01272954420780.4928636657760.07126291433910.005967762331830.744980287007-0.01532113892560.47117309056567.18763013655.2269965991913.995015244
641.96334814620.901455142766-0.4625826476431.351081281270.7570864608051.120736235930.1296863198160.19412138083-0.002349833836870.7266891491771.5223724038-0.6281233771081.00184090967-0.05496545611830.3136248135930.4597777110160.103916294111-0.08171920469670.7491512598260.2590474117631.0668828774582.72724619144.590648978467.6112981391
650.126088399049-0.0144561380343-0.08276664652390.0007018237122570.007859564666080.0378279653339-0.1026164390321.178040563910.3088649012430.4638908359450.0922884858847-0.311128072142-0.1348484691640.6856680165230.00164231091560.613081603505-0.0941788822201-0.01757317035070.666282867547-0.009373507784770.62740801268555.0063398936-36.2869935276.2419691019
660.376478049383-0.184928317787-0.2682776803221.16930433260.05970240838260.1689073586110.7536829805980.436445841827-1.40412116038-0.57593224599-0.1931326554460.175248413840.1292549067850.1678858569550.02578491067920.4156905792620.0350158609174-0.02665935979130.5711553294580.05060314233060.60286509212164.3365549313-43.061581860384.7386061826
670.3965599415990.145523442768-0.070303878760.1190286728550.002623586066670.0663730919455-0.7533452125220.843134677111-0.536529156114-0.4868885186970.642905484909-0.1811135656460.0879401165792-0.7027523074130.002226658436810.520298084095-0.0811612099507-0.03484004495170.5502114577590.1749212344430.69560435620829.2575473254-57.829936755263.9021673038
680.794457007311-1.0147633731-0.4344188102361.438251915230.4786652567330.3296649697260.2147771919070.202961485793-0.52663120483-0.25186991467-0.264859184447-0.9620652236930.07318860163140.09414271353610.0819979391690.801466751297-0.241149358839-0.2947159572320.4843292554290.06808057613481.2665608432135.0721842659-68.731237518769.2632708488
690.026496917924-0.1536799172380.08454982229960.284047715289-0.0356972108208-0.06563190497320.345570451083-0.4595566792820.3209311799380.3652893772980.1522640064-0.435752154232-0.2024513242980.1635444967860.001399908524630.48170661564-0.008463812289270.001351331259150.488197962278-0.113297695570.69550819935470.2283873442-13.620029701542.0366387093
700.3272660200060.5456874326171.04852900759-0.1783752634450.3217939001380.68966127381-0.1182510405380.04141641327010.2677466583860.0249031971110.08397637501690.321640310983-0.225554164796-0.0372083267815-0.001148186553750.409089248028-0.0448624005124-0.01547851504510.332508918065-0.01948851218080.43997645582944.9104376058-14.981593251935.6297774427
711.38345258169-0.973856154650.809422203621.283299152050.003857500831890.911324650296-0.383535238335-0.6626328751660.104152185532-0.1770402965380.006543039114050.220600624458-0.04893162075830.01312373884070.0001512874102620.4005613745140.0189009943953-0.03500466474980.322475063573-0.02955347117350.40814784039540.8821463094-8.448746459732.1550175878
720.2121333890690.02278698823380.4366224472690.238931010316-0.06286105405881.07313852665-0.1693439015990.292010848178-0.378776957002-0.2666340843630.1095657357110.1538383563610.1272752972120.117338393374-4.20076393247E-50.511152187381-0.00870305361321-0.05190079894050.427324028682-0.05340345063810.39044562953143.4569767382-14.682703875525.4890576418
730.66540494110.554060433391-0.1813811337560.558131603582-0.04131660485280.2177089123291.20715979691-0.147934032936-0.627493719016-0.6549651647520.0530847827484-0.6781550367850.2303105619671.331060025560.01782869860550.7445112995310.296852009762-0.06747507934310.6378497624560.03201499184050.88711641108158.7594278343-56.302310613729.645171523
740.1263673877740.0464292799505-0.09609605143610.1679455950660.1736280990460.2777215012130.2089944561220.175195980872-0.250350341148-0.213515851918-0.2032662551970.265860275142-0.393137896812-0.018595802991-0.0006168580872030.531776577608-0.0632160916904-0.09520439917580.43941062894-0.02759350478470.65190906719151.6174506638-43.016005696132.3304571969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'V' and (resid 30 through 57 )
2X-RAY DIFFRACTION2chain 'V' and (resid 58 through 84 )
3X-RAY DIFFRACTION3chain 'V' and (resid 85 through 98 )
4X-RAY DIFFRACTION4chain 'V' and (resid 99 through 103 )
5X-RAY DIFFRACTION5chain 'V' and (resid 104 through 118 )
6X-RAY DIFFRACTION6chain 'W' and (resid 14 through 20 )
7X-RAY DIFFRACTION7chain 'W' and (resid 21 through 29 )
8X-RAY DIFFRACTION8chain 'W' and (resid 30 through 57 )
9X-RAY DIFFRACTION9chain 'W' and (resid 58 through 84 )
10X-RAY DIFFRACTION10chain 'W' and (resid 85 through 91 )
11X-RAY DIFFRACTION11chain 'W' and (resid 92 through 98 )
12X-RAY DIFFRACTION12chain 'W' and (resid 99 through 103 )
13X-RAY DIFFRACTION13chain 'W' and (resid 104 through 118 )
14X-RAY DIFFRACTION14chain 'X' and (resid 18 through 29 )
15X-RAY DIFFRACTION15chain 'X' and (resid 30 through 57 )
16X-RAY DIFFRACTION16chain 'X' and (resid 58 through 84 )
17X-RAY DIFFRACTION17chain 'X' and (resid 85 through 103 )
18X-RAY DIFFRACTION18chain 'X' and (resid 104 through 112 )
19X-RAY DIFFRACTION19chain 'X' and (resid 113 through 118 )
20X-RAY DIFFRACTION20chain 'Y' and (resid 19 through 29 )
21X-RAY DIFFRACTION21chain 'Y' and (resid 30 through 57 )
22X-RAY DIFFRACTION22chain 'Y' and (resid 58 through 84 )
23X-RAY DIFFRACTION23chain 'Y' and (resid 85 through 98 )
24X-RAY DIFFRACTION24chain 'Y' and (resid 99 through 118 )
25X-RAY DIFFRACTION25chain 'B' and (resid 313 through 322 )
26X-RAY DIFFRACTION26chain 'B' and (resid 323 through 355 )
27X-RAY DIFFRACTION27chain 'B' and (resid 356 through 383 )
28X-RAY DIFFRACTION28chain 'B' and (resid 384 through 388 )
29X-RAY DIFFRACTION29chain 'C' and (resid 99 through 134 )
30X-RAY DIFFRACTION30chain 'C' and (resid 135 through 165 )
31X-RAY DIFFRACTION31chain 'D' and (resid 205 through 215 )
32X-RAY DIFFRACTION32chain 'D' and (resid 216 through 223 )
33X-RAY DIFFRACTION33chain 'E' and (resid 16 through 29 )
34X-RAY DIFFRACTION34chain 'E' and (resid 30 through 62 )
35X-RAY DIFFRACTION35chain 'E' and (resid 63 through 91 )
36X-RAY DIFFRACTION36chain 'E' and (resid 92 through 117 )
37X-RAY DIFFRACTION37chain 'F' and (resid 312 through 355 )
38X-RAY DIFFRACTION38chain 'F' and (resid 356 through 388 )
39X-RAY DIFFRACTION39chain 'G' and (resid 314 through 350 )
40X-RAY DIFFRACTION40chain 'G' and (resid 351 through 388 )
41X-RAY DIFFRACTION41chain 'H' and (resid 312 through 317 )
42X-RAY DIFFRACTION42chain 'H' and (resid 318 through 350 )
43X-RAY DIFFRACTION43chain 'H' and (resid 351 through 355 )
44X-RAY DIFFRACTION44chain 'H' and (resid 356 through 387 )
45X-RAY DIFFRACTION45chain 'I' and (resid 313 through 355 )
46X-RAY DIFFRACTION46chain 'I' and (resid 356 through 387 )
47X-RAY DIFFRACTION47chain 'J' and (resid 312 through 355 )
48X-RAY DIFFRACTION48chain 'J' and (resid 356 through 387 )
49X-RAY DIFFRACTION49chain 'K' and (resid 102 through 129 )
50X-RAY DIFFRACTION50chain 'K' and (resid 130 through 166 )
51X-RAY DIFFRACTION51chain 'L' and (resid 102 through 129 )
52X-RAY DIFFRACTION52chain 'L' and (resid 130 through 166 )
53X-RAY DIFFRACTION53chain 'M' and (resid 101 through 129 )
54X-RAY DIFFRACTION54chain 'M' and (resid 130 through 165 )
55X-RAY DIFFRACTION55chain 'N' and (resid 99 through 129 )
56X-RAY DIFFRACTION56chain 'N' and (resid 130 through 165 )
57X-RAY DIFFRACTION57chain 'O' and (resid 103 through 129 )
58X-RAY DIFFRACTION58chain 'O' and (resid 130 through 164 )
59X-RAY DIFFRACTION59chain 'P' and (resid 206 through 215 )
60X-RAY DIFFRACTION60chain 'P' and (resid 216 through 225 )
61X-RAY DIFFRACTION61chain 'Q' and (resid 206 through 215 )
62X-RAY DIFFRACTION62chain 'Q' and (resid 216 through 223 )
63X-RAY DIFFRACTION63chain 'R' and (resid 204 through 215 )
64X-RAY DIFFRACTION64chain 'R' and (resid 216 through 224 )
65X-RAY DIFFRACTION65chain 'A' and (resid 204 through 211 )
66X-RAY DIFFRACTION66chain 'A' and (resid 212 through 223 )
67X-RAY DIFFRACTION67chain 'T' and (resid 205 through 211 )
68X-RAY DIFFRACTION68chain 'T' and (resid 212 through 222 )
69X-RAY DIFFRACTION69chain 'U' and (resid 17 through 29 )
70X-RAY DIFFRACTION70chain 'U' and (resid 30 through 62 )
71X-RAY DIFFRACTION71chain 'U' and (resid 63 through 91 )
72X-RAY DIFFRACTION72chain 'U' and (resid 92 through 118 )
73X-RAY DIFFRACTION73chain 'V' and (resid 15 through 21 )
74X-RAY DIFFRACTION74chain 'V' and (resid 22 through 29 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more