[English] 日本語
Yorodumi
- PDB-7sol: Crystal Structures of the bispecific ubiquitin/FAT10 activating e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sol
TitleCrystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6
Components
  • Ubiquitin-like modifier-activating enzyme 6
  • Ubiquitin
KeywordsSIGNALING PROTEIN/Ligase / UBIQUITIN / E1 / ADENYLATION / THIOESTER BOND / E2 / FAT10 / IP6 / LIGASE / ATP-binding / nucleotide binding / conformational change / SIGNALING PROTEIN / SIGNALING PROTEIN-Ligase complex
Function / homology
Function and homology information


FAT10 activating enzyme activity / protein modification by small protein conjugation / amygdala development / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / thiosulfate sulfurtransferase activity / dendritic spine development / nucleotidyltransferase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / locomotory behavior ...FAT10 activating enzyme activity / protein modification by small protein conjugation / amygdala development / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / thiosulfate sulfurtransferase activity / dendritic spine development / nucleotidyltransferase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / locomotory behavior / learning / hippocampus development / modification-dependent protein catabolic process / protein tag activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / mRNA binding / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle ...Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25000635563 Å
AuthorsOlsen, S.K. / Gao, F. / Lv, Z.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115568 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128731 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR200030 United States
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6.
Authors: Yuan, L. / Gao, F. / Lv, Z. / Nayak, D. / Nayak, A. / Santos Bury, P.D. / Cano, K.E. / Jia, L. / Oleinik, N. / Atilgan, F.C. / Ogretmen, B. / Williams, K.M. / Davies, C. / El Oualid, F. / ...Authors: Yuan, L. / Gao, F. / Lv, Z. / Nayak, D. / Nayak, A. / Santos Bury, P.D. / Cano, K.E. / Jia, L. / Oleinik, N. / Atilgan, F.C. / Ogretmen, B. / Williams, K.M. / Davies, C. / El Oualid, F. / Wasmuth, E.V. / Olsen, S.K.
History
DepositionOct 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Apr 17, 2024Group: Atomic model / Derived calculations / Category: atom_site / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme 6
B: Ubiquitin
C: Ubiquitin-like modifier-activating enzyme 6
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,2617
Polymers248,9064
Non-polymers1,3543
Water15,259847
1
A: Ubiquitin-like modifier-activating enzyme 6
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4604
Polymers124,4532
Non-polymers1,0072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-19 kcal/mol
Surface area48890 Å2
MethodPISA
2
C: Ubiquitin-like modifier-activating enzyme 6
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8003
Polymers124,4532
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-15 kcal/mol
Surface area45270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.572, 101.317, 122.921
Angle α, β, γ (deg.)90.000, 117.996, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLUGLU(chain A and (resseq 59:204 or resseq 890:954))AA59 - 20427 - 172
121ILEILEILEILE(chain A and (resseq 59:204 or resseq 890:954))AA890 - 954858 - 922
211METMETGLUGLU(chain C and (resseq 59:204 or resseq 890:954))CC59 - 20427 - 172
221ILEILEILEILE(chain C and (resseq 59:204 or resseq 890:954))CC890 - 954858 - 922
132HISHISGLYGLY(chain B and resseq -3:76)BB-3 - 754 - 82
232HISHISGLYGLYchain DDD-3 - 754 - 82
143TRPTRPARGARG(chain A and resseq 955:1044)AA955 - 1044923 - 1012
243TRPTRPARGARG(chain C and resseq 955:1044)CC955 - 1044923 - 1012
154LYSLYSSERSER(chain A and (resseq 628:798 or resseq 819:889))AA628 - 798596 - 766
164GLUGLULYSLYS(chain A and (resseq 628:798 or resseq 819:889))AA819 - 889787 - 857
254LYSLYSSERSER(chain C and (resseq 628:798 or resseq 819:889))CC628 - 798596 - 766
264GLUGLULYSLYS(chain C and (resseq 628:798 or resseq 819:889))CC819 - 889787 - 857
175GLUGLUGLNGLN(chain A and resseq 212:290)AA212 - 290180 - 258
275GLUGLUGLNGLN(chain C and resseq 212:290)CC212 - 290180 - 258

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like ...Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like protein 2 / E1-L2


Mass: 114760.164 Da / Num. of mol.: 2 / Mutation: C625A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA6, MOP4, UBE1L2 / Plasmid: pFASTbac HTB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0AVT1, E1 ubiquitin-activating enzyme
#2: Protein Ubiquitin /


Mass: 9692.942 Da / Num. of mol.: 2 / Mutation: K6R, K11R, K27R, K29R, K33R, K48R, K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus / References: UniProt: P69326
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 3350, 0.2 M NaF

-
Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 125930 / % possible obs: 98 % / Redundancy: 4.75 % / Biso Wilson estimate: 39.0284861538 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.1
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 5797 / CC1/2: 0.777

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DC6
Resolution: 2.25000635563→45.9045852259 Å / SU ML: 0.250889902033 / Cross valid method: FREE R-VALUE / σ(F): 1.37070617071 / Phase error: 21.3182018971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205701836009 2000 1.59799292089 %
Rwork0.165797872043 123157 -
obs0.166435680207 125157 97.9955683268 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.0402852294 Å2
Refinement stepCycle: LAST / Resolution: 2.25000635563→45.9045852259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17106 0 0 847 17953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0040787528903717506
X-RAY DIFFRACTIONf_angle_d0.71761954282423751
X-RAY DIFFRACTIONf_chiral_restr0.04654745694712684
X-RAY DIFFRACTIONf_plane_restr0.005102268589033048
X-RAY DIFFRACTIONf_dihedral_angle_d10.400065055210685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.251-2.30630.274893211131340.2150101333288192X-RAY DIFFRACTION91.5649400638
2.3063-2.36860.2598406366321470.2128635099178494X-RAY DIFFRACTION95.3752759382
2.3686-2.43830.278878594581290.2068306789318686X-RAY DIFFRACTION97.3817940787
2.4383-2.5170.2395300534761480.2007272341358783X-RAY DIFFRACTION98.4349167861
2.517-2.6070.2473038744261460.1923630164918829X-RAY DIFFRACTION98.5289274344
2.607-2.71130.2460917355061330.1990932668628777X-RAY DIFFRACTION98.1169474727
2.7113-2.83470.2687773634861530.2011888200748755X-RAY DIFFRACTION97.9116289294
2.8347-2.98410.2506599697241400.2009112067138989X-RAY DIFFRACTION99.8577991687
2.9841-3.17110.2384227978471440.2000975204838908X-RAY DIFFRACTION99.7465564738
3.1711-3.41580.2697957897251450.190516868688932X-RAY DIFFRACTION99.5285087719
3.4158-3.75940.2095553488581450.1640552270838878X-RAY DIFFRACTION98.7955764809
3.7594-4.30310.1685681165191410.1351845402648834X-RAY DIFFRACTION97.9696539679
4.3031-5.42010.1504718513021450.125764761929007X-RAY DIFFRACTION99.7384481255
5.4201-45.90.149367934941500.1372479057419093X-RAY DIFFRACTION98.9190924658
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1182452692-0.041324453566-0.400181191081.50325333735-0.006597356671081.637706019790.0942689138035-0.6661791565360.1286090074150.254374447304-0.0684929364304-0.223767079493-0.0148096673840.4799455701890.004584372544520.298783171323-0.0996232372843-0.05945745634340.55539217144-0.04939113206850.32145562518153.563504012967.0266677254132.834177479
20.532184093163-0.158454523476-0.3527353345192.057832897351.23418203251.288974995-0.05237148487620.0936142073744-0.0363700648997-0.02945479333190.0111383559048-0.1168930932960.2835663795270.1935971297340.01928561499970.4504251390720.0881084620680.04503219977670.4980931189850.02735239332420.46707131435559.954949956641.0960646093103.187398803
31.36632089395-0.005119788478430.02821855557741.04764559881-0.01305450176230.9073823966070.0800922772655-0.004730888663730.4063845264540.0235313416687-0.067645474254-0.0426201093394-0.2310132946570.122785452426-0.03392410894030.316621347723-0.05732194835850.02053913934540.274312283605-0.03947295485940.35431335084440.685409029176.331528112118.325219142
41.248440864860.8780018066310.3848474169172.00682215115-0.9942809580892.675533322360.0805856102346-0.185910832711-0.07999841391640.142680147752-0.122336438848-0.2380717671550.06146008880570.3644951846140.03564056012570.303447311057-0.04537332444070.004060557055230.436347439150.01249914240990.22633682795732.556096088255.8354696346136.606750848
50.767582361834-0.1653767056130.008827152682870.718571454471-0.5353498132530.6699375453410.0724884799153-0.181099976065-0.1149084428570.0162494038949-0.0277145671530.07746481512670.125634896126-0.0590953628391-0.04887804276310.269801443166-0.0542434099218-0.01205291803190.2586016521620.02193091016250.25637421578726.480484711848.9793288794123.770860952
63.120132129910.0877279993138-0.8584056269742.2799279548-0.3653368710863.13426020115-0.0447430195557-0.242586862886-0.522815703203-0.0616823602427-0.12043018485-0.04847981236610.33946135292-0.07649964887290.1469514939820.4413043084650.007117281941840.01919503336840.3138304849030.07784285022950.53077302429643.125390832912.2776211079129.209702513
72.378493694870.71312044055-0.3466835063360.986928981665-0.4502033018880.982190726390.0397583091069-0.224532850906-0.296799307995-0.0479009380339-0.1036035766170.2188675611520.424076810867-0.1005874018470.06004356448060.5718386284910.0116433478470.01534612537860.338659940584-0.002803440282230.59219707510233.670936455610.764823167129.103834446
80.462262633217-0.477364633327-0.1454057615071.14029057169-0.2074939618230.0820299799121-0.105918683536-0.108819060418-0.174424261683-0.02694303589690.0339157283832-0.1026064941090.1425369419760.05934728289450.05909378296260.40120285666-0.01625867548270.01390001261950.3170487849450.04060246773290.37965649582344.755907764839.8418595077124.659275031
94.663204899292.088628665551.27785279421.043165535770.01292283649840.4293258904660.1022311972270.009964348529440.03400239107220.05264067451110.07919191461670.2359689866640.165056268813-0.0961809036282-0.1333894874730.32624498708-0.0847648084362-0.01455774414060.3119195690460.008723778239940.3466236579685.6873359469650.2316383817108.61470276
103.08652551223-0.09150193521650.1927805994992.697369879970.7948923743742.73480014511-0.2028610085330.154678946311-0.3121287838810.0979817645649-0.52420678272-0.8793644503180.4934799356980.4789593570920.4770127056920.8276624010730.1489709367790.09313436673240.970860383942-0.02900271015880.91239845781434.485276009657.346137503176.6328358199
115.086943431240.0279442239066-0.2954415097735.13067419175-1.351356297619.00370974643-0.2234591927891.4940577111-0.37882973327-0.69272285908-0.250352675746-0.3372733820410.05235936106670.4543876562290.3965049709280.4957641676310.1039866522530.07899619086840.716690286876-0.0310226296550.41712524954644.548037373353.037659268793.0503088805
122.160768160520.2488874822380.2733124017751.330132465920.5300849748340.2268818808590.1754400571581.29367039143-0.666061406981-0.3140530617330.009998726871730.07684953724160.189216258450.765283175489-0.05714705609040.3490288604430.108253120672-0.03433842448970.555568312526-0.1311360213660.33720894544942.398719454749.709882730895.8775694523
134.60212524713-1.7472514650.002331055987155.80872505502-0.6416395687473.98093214740.1155208667390.556046679501-0.85566248266-0.921796615587-0.360580608395-0.1466505760791.163121071660.2407294624050.2090621684430.5965134064250.0926075790922-0.008354284940540.456464342003-0.07970612080870.47410369726836.77419592544.060590503996.2271817493
141.87025017056-0.257597587812-0.3074638398242.455696634140.2006313111832.09863515771-0.0196954888921-0.0907050867717-0.434131191534-0.06386423369750.0582751749642-0.1540287440950.5348759244850.07776602567020.03873498900430.393995718954-0.0198178858293-0.03130724896060.3506315018520.004768564567270.3822048333834.285593147945.8469700002104.266514234
151.519102653171.002891856050.4245163388172.87759662290.7294211106224.440448103140.1095820977750.0352826989543-0.2042055168550.0580033133324-0.1296700443190.49358159166-0.129451593811-0.7446688415440.05320490142180.4025736115090.0434764912771-0.0732455134750.4002020035860.008451614513390.39547730632531.364227513756.471470139998.1907829043
162.138510147760.1424117657080.6244355057562.76205221015-0.8154090382962.946983163620.1428339938890.7249706019650.0468716836876-0.697639602301-0.23064187159-0.2261100577910.1931216129060.4955337591150.02824280036310.3309628917850.07763037487090.03351599108650.4009140233940.01533702666480.27916737784339.037679484657.315213944895.4824136838
173.20930696865-0.4982088189661.517366936571.27128989518-0.8697876054274.747364413290.20367672177-0.241295618649-0.9935501707480.285001668208-0.124520673604-0.139572488988-0.1794248084160.245575756849-0.2267679657730.2766203194760.013381362692-0.02806583296610.2809598740990.07004400493640.28859846059835.96011880947.4330365828117.703996614
181.814120251460.28481594721-0.3567208398311.87849385550.04110700217211.72414947038-0.05031401235640.3774344499020.0508125126413-0.4259194514870.02661822875770.0351107759306-0.134815112536-0.1754328502630.02324914046750.4487231288190.0324672915328-0.03050740625660.342369842899-0.01375080531950.24821839504721.144199287774.758269311446.7396567919
190.5017346943220.182454929667-0.05202367569660.962539696063-0.9983982988370.9703683636330.0545424623508-0.05635464435760.09049055840640.496838348897-0.114963943192-0.293368097928-0.5395250289760.267998680384-0.1054019740390.624596316553-0.101262515151-0.05985134648880.366239443537-0.01160198194480.39156931682138.251517926484.810407506369.3356348374
201.57917209617-0.163501353197-0.3288304666610.5476248586850.1352586780371.122790749440.05241630811380.0501889930192-0.0385617638516-0.0294187056025-0.05684913717830.181525838948-0.00663033586137-0.2556820606460.01030888062680.287853730147-0.00848025741404-0.02403507037230.279303565768-0.005891041175720.2638064385810.344995279469.807223182667.2944970517
211.913780755310.144219518175-0.5025573812980.887460040490.0004512238973310.07574945400460.07802781430850.5665558716050.423287321461-0.105216294095-0.05729533934010.161578650954-0.0642009488062-0.240501654861-0.01818411046980.3844055660910.0460198188119-0.01530651417880.4800508015750.0453031446050.3529774176835.0955648382694.521753465762.037748535
221.42147459446-0.0327579644924-0.2981512323310.388039479337-0.2005969318130.6389151157050.1197248455860.2445127905620.436937315036-0.035461602242-0.05019829896320.123485581017-0.155377201633-0.116781344207-0.05891662590230.335204715280.00321517276694-0.006998877548170.2957973690010.005448955939190.4062659112236.8496430440795.097913162969.9234564084
232.288846615290.53478126396-0.06455962444382.230514258590.01975312006442.413726751020.02189388946-0.1818923276760.5470311784280.202706482199-0.006418200898190.521002738359-0.171917879825-0.6958460422070.05211362779030.2966113859440.08061845265330.05175786616850.3715678753280.02796674810030.472562627291.4654213313875.2392364403108.68441445
246.62859404515-2.507307411740.6017212396265.99796248321-0.1701871962861.49540853116-0.432737636295-0.03915028605310.6152536052570.652030964163-0.0105818914374-0.947368692545-0.06533595416541.105197515730.4017239905110.624768754195-0.0486505666957-0.116395931150.6606210313890.1174635434910.59903649739744.804924990477.915140880688.6543937188
252.4240499379-0.4487120013440.8141800705072.15087553012-0.5982085306053.43250224631-0.126742397642-0.2114757143670.2719023997660.500158908088-0.173380321812-0.36902542817-0.3982523411330.3583999308670.2396119939890.445865709128-0.0663011066152-0.05795680234080.374098663520.01883918719650.32739383787434.450161967678.478918980787.9866194279
268.36211504635-3.25101369734.142875566896.4367673293-3.744380445899.10813589050.671778294129-0.0727104669713-0.0504271322927-0.1814853491430.1172839894370.456035654747-0.511265866745-0.214144394502-0.7198402441920.3695273992640.05047729510180.09474883755290.304289895767-0.01885883870560.2922406936116.887607198283.501922931477.8018811294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 469 )
4X-RAY DIFFRACTION4chain 'A' and (resid 470 through 520 )
5X-RAY DIFFRACTION5chain 'A' and (resid 521 through 633 )
6X-RAY DIFFRACTION6chain 'A' and (resid 634 through 797 )
7X-RAY DIFFRACTION7chain 'A' and (resid 798 through 857 )
8X-RAY DIFFRACTION8chain 'A' and (resid 858 through 913 )
9X-RAY DIFFRACTION9chain 'A' and (resid 914 through 1050 )
10X-RAY DIFFRACTION10chain 'B' and (resid -6 through -1 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 6 )
12X-RAY DIFFRACTION12chain 'B' and (resid 7 through 22 )
13X-RAY DIFFRACTION13chain 'B' and (resid 23 through 34 )
14X-RAY DIFFRACTION14chain 'B' and (resid 35 through 44 )
15X-RAY DIFFRACTION15chain 'B' and (resid 45 through 56 )
16X-RAY DIFFRACTION16chain 'B' and (resid 57 through 70 )
17X-RAY DIFFRACTION17chain 'B' and (resid 71 through 76 )
18X-RAY DIFFRACTION18chain 'C' and (resid 59 through 198 )
19X-RAY DIFFRACTION19chain 'C' and (resid 199 through 364 )
20X-RAY DIFFRACTION20chain 'C' and (resid 365 through 584 )
21X-RAY DIFFRACTION21chain 'C' and (resid 585 through 731 )
22X-RAY DIFFRACTION22chain 'C' and (resid 732 through 967 )
23X-RAY DIFFRACTION23chain 'C' and (resid 968 through 1048 )
24X-RAY DIFFRACTION24chain 'D' and (resid -3 through 6 )
25X-RAY DIFFRACTION25chain 'D' and (resid 7 through 70 )
26X-RAY DIFFRACTION26chain 'D' and (resid 71 through 76 )

+
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