[English] 日本語
Yorodumi
- PDB-6niu: Crystal structure of a human anti-ZIKV-DENV neutralizing antibody... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6niu
TitleCrystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ4 in complex with ZIKV E glycoprotein
Components
  • Envelope protein E
  • Human MZ4 Fab heavy chain
  • Human MZ4 Fab light chain
KeywordsViral protein/IMMUNE SYSTEM / ZIKV-DENV / Antibody / human / Vaccination / ANTIVIRAL PROTEIN / IMMUNE SYSTEM / Viral protein-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / molecular adaptor activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Zika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.303 Å
AuthorsSankhala, R.S. / Dussupt, V. / Donofrio, G. / Choe, M. / Modjarrad, K. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentW81XWH-07-2-0067 United States
CitationJournal: Nat. Med. / Year: 2020
Title: Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor.
Authors: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / ...Authors: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / Abbink, P. / Bai, H. / Bryan, A.L. / Bias, C.H. / Berry, I.M. / Botero, N. / Cook, T. / Doria-Rose, N.A. / Escuer, A.G.I. / Frimpong, J.A. / Geretz, A. / Hernandez, M. / Hollidge, B.S. / Jian, N. / Kabra, K. / Leggat, D.J. / Liu, J. / Pinto, A.K. / Rutvisuttinunt, W. / Setliff, I. / Tran, U. / Townsley, S. / Doranz, B.J. / Rolland, M. / McDermott, A.B. / Georgiev, I.S. / Thomas, R. / Robb, M.L. / Eckels, K.H. / Barranco, E. / Koren, M. / Smith, D.R. / Jarman, R.G. / George, S.L. / Stephenson, K.E. / Barouch, D.H. / Modjarrad, K. / Michael, N.L. / Joyce, M.G. / Krebs, S.J.
History
DepositionDec 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Feb 26, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Human MZ4 Fab heavy chain
L: Human MZ4 Fab light chain
B: Envelope protein E
A: Envelope protein E
Z: Envelope protein E
E: Envelope protein E
F: Human MZ4 Fab heavy chain
G: Human MZ4 Fab light chain
I: Human MZ4 Fab heavy chain
J: Human MZ4 Fab light chain
M: Human MZ4 Fab heavy chain
N: Human MZ4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)293,39612
Polymers293,39612
Non-polymers00
Water0
1
H: Human MZ4 Fab heavy chain
L: Human MZ4 Fab light chain
Z: Envelope protein E
E: Envelope protein E
M: Human MZ4 Fab heavy chain
N: Human MZ4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)146,6986
Polymers146,6986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope protein E
A: Envelope protein E
F: Human MZ4 Fab heavy chain
G: Human MZ4 Fab light chain
I: Human MZ4 Fab heavy chain
J: Human MZ4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)146,6986
Polymers146,6986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.530, 137.260, 136.790
Angle α, β, γ (deg.)80.120, 65.740, 65.750
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain E
41chain Z
12chain F
22chain H
32chain I
42chain M
13chain G
23chain J
33chain L
43chain N

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSERchain AAD1 - 4031 - 403
21ILEILESERSERchain BBC1 - 4031 - 403
31ILEILESERSERchain EEF1 - 4031 - 403
41ILEILESERSERchain ZZE1 - 4031 - 403
12GLNGLNSERSERchain FFG1 - 1131 - 120
22GLNGLNSERSERchain HHA1 - 1131 - 120
32GLNGLNSERSERchain III1 - 1131 - 120
42GLNGLNSERSERchain MMK1 - 1131 - 120
13GLNGLNLEULEUchain GGH1 - 1071 - 111
23GLNGLNLEULEUchain JJJ1 - 1071 - 111
33GLNGLNLEULEUchain LLB1 - 1071 - 111
43GLNGLNLEULEUchain NNL1 - 1071 - 111

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody
Human MZ4 Fab heavy chain


Mass: 13219.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Details (production host): pVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody
Human MZ4 Fab light chain


Mass: 11731.954 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Details (production host): pVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein
Envelope protein E /


Mass: 48397.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 / Details (production host): pMT-BiP / Cell line (production host): DS2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A024B7W1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.65 % / Description: Plate like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.26 M ammonium sulfate, 0.1 M CHES/NaOH (pH 9.5) and 0.2 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 16201 / % possible obs: 53.2 % / Redundancy: 1.6 %
Details: The diffraction data was corrected for anisotropy using diffraction anisotropy correction server, which resulted in less reflections for refinement
Rpim(I) all: 0.23 / Rsym value: 0.23 / Net I/σ(I): 2.64
Reflection shellResolution: 4.2→4.35 Å / Num. unique obs: 2954 / Rsym value: 0.515

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTA, 5IRE

4uta

5ire


Resolution: 4.303→9.997 Å / SU ML: 0.96 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 45.06
RfactorNum. reflection% reflection
Rfree0.359 629 4.96 %
Rwork0.2641 --
obs0.2689 12689 29.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 387.47 Å2 / Biso mean: 142.9901 Å2 / Biso min: 18.39 Å2
Refinement stepCycle: final / Resolution: 4.303→9.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19232 0 0 0 19232
Num. residues----2520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4828X-RAY DIFFRACTION1.298TORSIONAL
12B4828X-RAY DIFFRACTION1.298TORSIONAL
13E4828X-RAY DIFFRACTION1.298TORSIONAL
14Z4828X-RAY DIFFRACTION1.298TORSIONAL
21F1448X-RAY DIFFRACTION1.298TORSIONAL
22H1448X-RAY DIFFRACTION1.298TORSIONAL
23I1448X-RAY DIFFRACTION1.298TORSIONAL
24M1448X-RAY DIFFRACTION1.298TORSIONAL
31G1340X-RAY DIFFRACTION1.298TORSIONAL
32J1340X-RAY DIFFRACTION1.298TORSIONAL
33L1340X-RAY DIFFRACTION1.298TORSIONAL
34N1340X-RAY DIFFRACTION1.298TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.303-4.69490.3676290.21125135425
4.6949-5.28460.3256890.22921805189418
5.2846-6.35930.36552090.26424228443742
6.3593-9.9970.36453020.28115514581654
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)
10.02410.003-0.00840.00460.0007-0.0008-0.15850.0170.09820.12780.05360.04910.19410.0754-0.00030.45930.15270.07920.55920.26291.2312-80.9185.72584.491
20.0092-0.0034-0.00130.00350.00720.00580.1878-0.07640.0664-0.0550.14410.0374-0.0959-0.0194-0.00051.0925-0.49890.19690.91050.22750.9687-72.91764.28288.204
30.1224-0.03470.03040.016-0.007-0.00170.73210.12250.0921-0.17380.1557-0.0025-0.26780.08530.05530.84760.36950.08720.56320.11310.4969-74.43986.80986.324
40.2610.10570.17470.1352-0.11550.5134-0.19360.30830.0647-0.1094-0.14680.0435-0.3570.3393-0.03660.8413-0.0760.10830.7874-0.41231.6685-73.83482.08397.397
50.06740.06340.08070.07680.09690.1019-0.0856-0.17440.1116-0.4041-0.0284-0.0794-0.259-0.00150.01041.4457-0.5475-0.19530.44190.53431.2154-67.6577.51197.398
6-0.00360.00040.01180.0039-0.01380.0241-0.26370.3057-0.11160.05590.05850.1405-0.17970.2733-0.0010.1585-0.25820.19680.586-0.08360.7726-69.39782.61885.988
70.02430.00710.00420.0007-0.00640.0104-0.05190.0006-0.03140.11220.11730.1133-0.04070.04080.00010.8759-0.3276-0.03671.34960.00180.5327-73.8865.76896.353
80.0939-0.00360.0198-0.00110.00320.0078-0.12680.090.1238-0.02060.02020.0405-0.0352-0.02660.05670.99280.2832-0.44350.8832-0.11410.5566-80.3679.59993.469
90.9721-1.1489-0.0421.5142-0.34690.83640.06880.7934-0.7088-0.3015-0.14880.6740.2441-0.4095-0.224-0.2160.3731-0.29020.95870.36280.9519-79.72493.54494.645
106.5071.3653-0.41314.6658-2.45653.4163-0.12970.0159-0.5827-0.03470.05690.89350.27580.3059-0.12070.28740.3938-0.1430.799-0.3111.2579-80.41566.00390.375
110.22170.0098-0.07270.2060.10490.0761-0.12660.04030.00370.0072-0.0933-0.01760.17050.1662-0.15960.4096-0.68140.16120.61320.38830.9489-84.49581.604112.948
120.0092-0.00690.00990.03920.00660.00160.05250.0266-0.03710.08890.0588-0.02750.0106-0.03310.0321.4520.71190.1320.6952-1.20841.0249-105.67386.089109.875
130.0597-0.00110.0162-0.0028-0.00280.00260.0187-0.01750.0103-0.03540.07040.1107-0.0785-0.0624-0.00011.2734-0.4466-0.42091.40930.18071.6342-92.92687.737112.703
140.0799-0.0364-0.03810.0525-0.01920.0374-0.01560.1947-0.026-0.3225-0.47170.1170.22430.4575-0.05540.17640.4412-0.33390.9584-0.09981.161-82.79690.137108.219
150.0706-0.0268-0.11280.11650.06810.18-0.0186-0.2087-0.0189-0.02330.03740.0039-0.31160.01120.11520.5334-0.2243-0.51561.04990.18270.7577-91.33783.99296.338
160.14220.00140.07760.02960.0390.08290.0670.11690.0801-0.0721-0.0119-0.0539-0.01580.00560.09910.862-0.5631.15750.49770.08230.8549-90.30697.91599.537
170.03580.00680.04060.02530.00690.0558-0.01470.19180.01070.08950.0532-0.0964-0.0581-0.2605-0.00110.18910.2362-0.0390.4247-0.21750.7145-96.45495.022104.03
180.0917-0.01080.02890.037-0.02660.02440.0361-0.02920.021-0.13410.12840.07690.0117-0.0430.04490.972-0.49940.51711.11830.4350.9108-90.62492.347112.5
190.0251-0.0111-0.03120.14490.05360.0526-0.00660.1131-0.0045-0.0949-0.0863-0.1050.10950.1206-0.02790.93650.4552-0.34580.83150.00331.1116-103.96385.304101.535
200.15260.0424-0.11250.0809-0.02190.07820.1715-0.01360.11710.01690.2755-0.1613-0.0862-0.1040.28710.51340.2680.82170.73720.00140.8321-84.87185.43105.281
210.4169-0.7274-0.08511.28650.12280.1196-0.17890.1868-0.0925-0.598-0.02710.55160.49470.0455-0.56381.3405-0.0582-0.5692-0.38290.08620.5345-77.47284.687107.212
220.22620.0141-1.05065.812-0.35874.88880.02240.23120.03360.4344-0.22280.9447-0.1898-1.34190.16780.7921-0.10780.4780.972-0.25140.547-103.60579.041107.781
231.7126-0.7271-0.05941.5128-0.37630.1510.1431-0.067-0.32640.70720.36770.61690.2310.45120.01091.11070.4379-0.09181.1545-0.37550.8348-115.47868.31383.213
241.2080.3467-0.16631.8474-0.48593.14990.2616-0.13060.19680.47510.4891-0.15080.36480.75960.20540.96510.11640.47330.7412-0.72640.6759-61.29269.05868.979
250.4222-0.99110.51792.5159-1.31321.02040.12780.0672-0.1680.63910.7322-0.28470.01330.7167-0.12571.27760.2405-0.55960.4632-0.10171.1973-47.20762.50267.882
260.39010.319-0.11250.31930.02270.72330.48760.3749-0.34480.74240.25840.2709-0.7540.32490.23630.6367-0.4509-0.15281.4720.31611.0946-81.15672.28273.236
271.1860.4357-1.04840.4915-0.73981.42880.03620.50190.2741-0.6203-0.4565-0.2035-1.1454-0.2830.62151.2155-0.2126-0.14480.9642-0.24271.3389-114.87881.03774.697
281.6697-0.0602-1.07870.11650.65512.03520.9317-0.70170.09790.15240.3626-0.00271.02330.9585-0.2830.6332-0.070.05270.66380.39721.1532-79.30265.35572.959
290.5219-0.35370.02790.6131-0.19320.1665-0.0826-0.7133-0.00040.38540.5060.02050.22420.32770.36520.6022-0.69450.19290.54490.920.1208-120.0772.1376.609
300.2430.0538-0.09760.0165-0.03540.2426-0.382-0.1420.35350.1170.0656-0.0862-0.2073-0.05570.10.53680.2760.02860.51930.15791.4039-137.71267.16175.314
310.8088-0.2841-0.44281.4323-0.04420.3734-0.1948-0.30270.2909-0.3144-0.4105-0.2380.19310.2427-0.13610.70370.5652-0.03730.61740.48781.0529-135.42865.06471.964
323.4744-1.40490.92321.18580.51290.6955-0.2427-0.02160.43920.30260.1944-0.38630.1423-0.1308-0.00420.817-0.06140.11690.3876-0.04511.196-69.19546.79451.133
330.73120.6596-0.25910.99450.70932.4747-0.19010.3154-0.0150.1376-0.1481-0.33320.0028-0.37070.33360.7726-0.00870.10080.73380.08460.9749-24.78545.86852.155
340.7121-0.88310.07391.2940.32140.26250.87150.46170.2962-0.04381.02520.4192-0.6347-0.52440.12850.5896-0.0445-0.2310.89020.31470.5753-59.161115.02299.551
350.5014-0.6411-0.33741.0031-0.0741.502-0.62230.31870.43580.31740.00780.1129-0.02710.1399-0.7082-0.17890.2268-0.39291.90140.18460.9988-4.563114.401114.009
360.29440.37970.37470.1184-0.01931.11060.7514-0.0767-0.41320.04380.19740.01660.01870.97170.75880.7490.3425-0.47210.00580.68630.4039-26.088114.171109.933
370.8606-0.25880.00880.5296-0.04071.0516-0.1731-0.09590.27460.052-0.1355-0.36680.65390.08980.46260.43370.0112-0.44030.52530.36330.8051-69.213111.52107.128
380.420.4481-0.09220.84620.61260.9987-0.40840.62350.8972-0.1382-0.2450.49710.608-0.2430.13610.41290.23650.09740.94130.49610.7141-80.31119.578107.089
393.2119-1.46280.71150.685-0.48181.33320.56311.00990.4447-0.8276-0.6605-0.5309-0.46540.4893-0.34392.13090.35140.04870.7466-0.19270.813616.317147.591128.816
402.819-1.3740.05421.5804-1.11451.2240.2717-0.3038-0.46950.2592-0.0170.06190.75990.5075-0.27010.5513-0.37010.06391.1992-0.64921.362-28.763131.207133.296
410.83360.35830.03071.09020.61480.59070.22170.1940.2252-0.3626-1.0560.6491-1.0681-1.172-0.30480.0441-0.69361.10570.22620.30210.3146-36.182133.419128.914
423.4705-2.1783-2.0062.43941.71686.8852-0.06090.1036-0.43960.12030.02170.2910.5891-0.28380.07170.4758-0.44670.4481.39770.06020.922720.515133.165139.997
431.30380.35620.97320.5484-0.16570.90440.2230.18190.2666-0.36530.35440.3101-0.5694-0.60840.88770.5370.6175-0.35390.46970.1335-0.5582-0.647144.547135.154
443.29610.34490.03452.78240.9732.0099-0.1873-0.14590.4142-0.30060.1338-0.67220.28070.0672-0.32340.8073-0.20310.34480.8082-0.45481.2091-35.012130.723125.989
450.81610.17330.11670.8428-0.32180.71410.69230.5140.2018-0.6776-0.4305-0.07870.06160.2160.41621.05320.0362-0.59990.92820.37350.80652.57140.247131.891
461.13830.1143-0.1310.64680.96951.6803-0.02770.73191.26820.0048-0.1685-1.1394-0.9323-0.1331-0.0869-0.3573-0.0692-0.22971.802-0.02941.293437.428137.567126.981
471.93960.40690.30341.42750.23020.89940.20060.03060.3828-0.77440.32940.2368-0.2105-0.0846-0.01630.34780.05610.17471.2514-0.36082.633136.791136.296125.207
480.0345-0.06260.00760.1257-0.02950.0824-0.14820.16490.07960.0159-0.2845-0.0123-0.15-0.0516-0.43290.8417-0.1801-0.64961.05070.15860.7856-139.31199.79398.126
490.00390.0069-0.00120.00130.00470.0074-0.0048-0.0421-0.0085-0.0928-0.1985-0.0515-0.0258-0.03720.00011.12570.3047-0.34061.3383-0.02590.811-129.384119.89893.24
5010.82660.13220.67720.10070.0142-0.0484-0.01390.0624-0.02180.0360.0090.0453-0.03350.05240.3114-0.2099-0.55730.01130.11880.2788-131.394105.37695.485
510.00010.00130.0027-0.0001-0.0010.0007-0.03720.0421-0.07990.0795-0.01560.06560.06660.074-0.0320.9041-0.4835-0.90310.9858-0.25850.7727-132.37290.38295.045
520.0289-0.03490.09470.013-0.0780.6129-0.182-0.1694-0.19510.1619-0.05460.0438-0.2173-0.1730.00921.1582-0.3602-0.10520.41950.2031.2577-133.165101.88186.183
530.30440.3505-0.29580.4117-0.35280.2724-0.2952-0.0919-0.1272-0.1421-0.4215-0.1663-0.14970.3415-0.05710.6437-0.2161-0.20681.8659-0.0340.7632-135.382106.73981.306
540.005-0.0063-0.00180.0323-0.02670.011-0.39630.08770.0088-0.0954-0.24590.2297-0.2937-0.11670.00041.5735-0.710.0681.83890.18762.3288-122.34896.04385.714
550.3229-0.36530.26790.4166-0.31260.23330.42620.35720.4586-0.0651-0.0156-0.1554-0.0785-0.16420.06190.8691-0.83660.6471.03120.14340.5366-124.378106.64384.179
560.08910.0931-0.01440.2746-0.07140.0224-0.0073-0.2521-0.19570.1028-0.08360.02020.21730.00640.01110.5976-0.3164-0.68590.4253-0.8890.3934-126.688101.82395.639
570.0156-0.07270.01830.3077-0.08730.0216-0.2093-0.091-0.08850.29650.14690.10460.13950.26050.06980.94810.07090.12670.8628-0.07530.2294-134.113110.99486.498
583.28682.4432-1.42194.637-2.72155.26360.51210.11921.49950.79320.22351.2145-1.5063-0.4568-0.60070.7565-0.87140.49180.45230.57731.1893-136.79690.94786.842
596.7569-3.68662.45592.50710.19087.26040.17520.17810.0519-0.1538-0.1412-0.23510.25450.20220.05350.3308-0.02880.23070.8440.75030.6377-136.93118.26790.645
600.0045-0.00710.00770.0174-0.00910.00110.14760.0227-0.00330.09920.20760.1519-0.1228-0.072401.04270.2901-0.12351.2235-0.02271.5568-141.599102.88667.886
610.4080.00150.38350.272-0.08560.39810.1213-0.08360.07980.1480.0986-0.0812-0.129-0.15030.22640.57650.09520.0260.8523-0.33990.3731-161.80698.7871.388
620.0477-0.0680.04460.081-0.08310.2273-0.19310.10980.02190.2312-0.0287-0.0653-0.10060.1626-0.02530.9425-0.07630.36590.6713-0.540.5526-139.4593.85268.362
630.00330.0027-0.00440.0043-0.00540.00960.05070.0204-0.0474-0.022-0.0654-0.10890.0412-0.01190.010.9887-0.0948-0.05010.60950.09391.0587-145.68496.98179.321
640.00440.00260.00880.01170.00080.0003-0.2098-0.08090.05190.1555-0.0270.03190.0298-0.07260.00040.6050.0324-0.02540.8179-0.27111.0086-147.93699.8286.068
650.03750.11230.04870.31470.05090.1515-0.0912-0.0450.0105-0.1969-0.0804-0.02430.2721-0.0311-0.13570.64230.4205-0.03380.5034-0.86750.3911-149.186.26183.318
660.2179-0.0982-0.00240.0978-0.08570.1068-0.027-0.1103-0.02480.31530.25470.1706-0.3284-0.15210.06740.55120.5925-0.18570.3046-0.21140.4861-148.07790.45671.858
670.2769-0.33990.19690.4691-0.23230.14210.0844-0.1920.10150.4067-0.00170.1577-0.3943-0.1129-0.10560.7167-0.42170.26360.5950.10380.6693-160.65999.1880.029
680.09570.17520.21740.72020.19810.6277-0.07310.12870.1356-0.1735-0.09590.09730.0068-0.0074-0.43810.75910.2869-0.22531.1445-0.96230.9152-136.20798.52374.791
690.5244-0.0051-0.74230.131-0.07911.11230.0042-1.5487-1.0291-0.03880.40070.4610.2859-0.9851-0.94910.4277-0.3338-0.06941.46110.76010.7529-139.711101.78974.556
700.83110.3120.1170.3682-0.06670.06610.0757-0.40760.034-0.2031-0.50730.59720.1761-0.43360.19851.0611-0.5581-0.66981.5917-0.4731.0424-160.386105.26973.954
710.0399-0.0083-0.01030.0129-0.00480.00190.07030.12970.4716-0.08810.09850.1104-0.1004-0.0167-0.00070.93760.48450.05161.43050.20260.1859-21.28324.2111.785
72-0.00280.00810.01410.01720.03050.03920.2473-0.0968-0.24050.0846-0.027-0.12110.2230.13110.17420.7616-0.2119-1.06950.76920.1980.5845-23.4124.71623.963
730.1833-0.2397-0.27940.29720.35420.3509-0.27520.36210.03070.0485-0.5603-0.02270.1020.4703-0.06840.29110.0643-0.39990.77410.06990.7157-20.10835.90516.643
740.3066-0.1925-0.37270.12430.25290.4948-0.3289-0.5816-0.1520.1725-0.04850.06630.343-0.0227-0.28940.52870.0681-0.29541.47010.65420.5811-31.20935.00418.37
750.0922-0.05570.06950.0228-0.03480.02020.2427-0.13410.36440.26340.2270.0909-0.0802-0.5422-0.00030.6812-0.093-0.05791.1798-0.19321.1217-23.82329.09714.365
761.5692-1.42740.86771.4472-0.76260.73710.05040.37140.4221-0.0054-0.0637-0.1092-0.1896-0.10170.2207-0.12590.20750.24130.7780.69710.8267-19.76735.04934.343
770.2785-0.2966-0.00040.5217-0.06570.015-0.10070.554-0.2245-0.3105-0.49250.10590.32180.43950.23250.9267-0.09410.33771.11510.5541.6963-15.74828.1311.559
780.2312-0.0899-0.07380.1299-0.077-0.0113-0.2809-0.2763-0.0609-0.16090.09960.04520.079-0.48020.321-0.2616-1.10870.9837-1.18830.7846-0.3601-9.00248.60823.278
79-0.00560.0023-0.00410.0492-0.01810.0080.07510.1481-0.0088-0.0205-0.12810.041-0.065-0.0046-0.03530.7150.3607-0.00420.3674-0.86840.8897-7.59734.74723.002
800.4209-0.01780.03130.13310.06550.04070.2507-0.1808-0.1603-0.0990.20120.0541-0.0151-0.1050.25130.6207-0.15920.2070.4717-0.11560.6702-4.83537.10334.6
811.5594-0.75750.26010.8379-0.04540.5213-0.16350.2956-0.1467-0.0376-0.21710.076-0.25770.53110.61420.5847-0.0636-0.39780.25150.0680.8891-8.10544.9223.165
820.17770.05580.0203-0.00010.01390.2417-0.1128-0.3941-0.39110.20650.2670.11630.05280.00780.22850.63520.28620.4652-0.4283-0.56410.607134.087159.475168.855
830.27020.1104-0.09570.233-0.06290.13590.02730.03550.0227-0.0515-0.05870.01310.0318-0.0209-0.0820.3715-0.2629-0.54151.4189-0.02150.911732.152158.176150.741
840.3734-0.0925-0.2910.3089-0.08450.33930.15620.23810.2228-0.07830.11170.0455-0.2723-0.23780.32150.87360.01710.10540.4731-0.45281.138634.139150.077163.019
850.56250.0430.18760.00040.01070.5689-0.1059-0.1367-0.0734-0.0406-0.1404-0.08950.18630.399-0.08960.5081-0.87570.08410.45350.25591.124536.317145.3168.05
86-0.00430.00190.00160.0045-0.01580.00480.098-0.0104-0.0037-0.2693-0.15180.0416-0.1585-0.1166-0.00041.6040.3830.52131.1985-0.23981.494823.346149.901157.072
870.0956-0.015-0.04870.00130.0310.20010.00830.29870.18910.04690.07530.16710.0067-0.28040.2752-0.2216-0.26450.62040.98040.49830.367225.517148.225167.701
880.188-0.01510.0570.06180.05120.0347-0.10830.04280.1467-0.30290.07690.1991-0.2083-0.08320.02791.0101-0.63840.01110.33880.38861.097728.711155.542169.17
890.00460.0032-0.01420.009-0.01680.02620.04830.06990.0394-0.0401-0.03240.1458-0.02390.06430.01540.4648-0.44090.15970.6035-0.11260.603238.101152.047165.637
902.6145-1.23790.44523.6738-1.02621.5159-0.4809-0.72080.37441.50510.1734-0.8905-0.62290.13670.16170.58940.1909-0.14790.19590.26130.433437.797149.311152.349
912.987-0.42032.15855.2389-1.34819.8216-0.0783-0.0403-0.062-0.20820.0875-0.01910.05150.35670.02280.68240.10770.10141.15550.39271.70737.935155.365179.249
920.00290.0043-0.00350.0168-0.00860.0062-0.1154-0.0396-0.05540.0735-0.0437-0.03120.01670.0187-0.00011.1022-0.36760.13571.03720.0661.610843.073130.04166.328
930.0048-0.0042-0.00840.0290.02480.0085-0.0056-0.0532-0.02120.00320.02480.04750.0291-0.0524-0.00620.32570.2629-0.13160.61470.10830.862358.511134.201160.263
940.0178-0.00770.00530.020.01520.0267-0.0057-0.0027-0.0112-0.00490.0872-0.1319-0.05240.20220.01620.4357-0.2074-0.21451.71150.41631.021135.467132.281153.649
950.14380.0364-0.01740.0356-0.0086-0.00060.01060.1596-0.04260.1188-0.0929-0.0122-0.0378-0.076-0.03780.2572-0.1307-0.3354-0.2009-0.59590.426246.928143.2158.482
960.02880.0337-0.0130.0306-0.01330.00550.019-0.25810.0296-0.01370.0324-0.1551-0.04210.0474-0.06280.5307-0.1781-0.6433-0.0467-0.25860.976948.712149.44161.664
970.0122-0.01620.0380.0142-0.06080.27530.0215-0.09890.14560.00320.0550.0746-0.1690.01310.23730.4730.04680.35620.49-0.03670.769850.331146.769147.824
98-0.00150.00150.00230.0661-0.15480.34870.21680.09020.0652-0.11390.2744-0.0773-0.011-0.1890.06070.77310.1390.3109-0.2808-0.01710.521149.397135.184152.109
990.03040.0236-0.02210.06950.02570.0404-0.14940.0569-0.03120.1974-0.02880.00440.0048-0.0203-0.14290.46920.07490.579-0.0972-0.58840.557561.676144.288160.498
1000.06560.0050.0122-0.0049-0.010.04570.03030.08160.0495-0.05-0.0924-0.2022-0.0390.0518-0.03490.8118-0.3318-0.84641.23050.41880.459642.89140.075160.297
1010.9866-0.3511-0.40711.17890.47841.0059-0.0604-0.2290.0693-0.06460.74950.01970.39740.50780.25461.37420.33350.00790.3859-0.67860.374442.782138.254162.955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:8 )H1 - 8
2X-RAY DIFFRACTION2( CHAIN H AND RESID 9:17 )H9 - 17
3X-RAY DIFFRACTION3( CHAIN H AND RESID 18:32 )H18 - 32
4X-RAY DIFFRACTION4( CHAIN H AND RESID 33:59 )H33 - 59
5X-RAY DIFFRACTION5( CHAIN H AND RESID 60:72 )H60 - 72
6X-RAY DIFFRACTION6( CHAIN H AND RESID 73:82 )H73 - 82
7X-RAY DIFFRACTION7( CHAIN H AND RESID 83:87 )H83 - 87
8X-RAY DIFFRACTION8( CHAIN H AND RESID 88:95 )H88 - 95
9X-RAY DIFFRACTION9( CHAIN H AND RESID 96:106 )H96 - 106
10X-RAY DIFFRACTION10( CHAIN H AND RESID 107:113 )H107 - 113
11X-RAY DIFFRACTION11( CHAIN L AND RESID 1:8 )L1 - 8
12X-RAY DIFFRACTION12( CHAIN L AND RESID 9:18 )L9 - 18
13X-RAY DIFFRACTION13( CHAIN L AND RESID 19:24 )L19 - 24
14X-RAY DIFFRACTION14( CHAIN L AND RESID 25:38 )L25 - 38
15X-RAY DIFFRACTION15( CHAIN L AND RESID 39:48 )L39 - 48
16X-RAY DIFFRACTION16( CHAIN L AND RESID 49:58 )L49 - 58
17X-RAY DIFFRACTION17( CHAIN L AND RESID 59:66 )L59 - 66
18X-RAY DIFFRACTION18( CHAIN L AND RESID 67:75 )L67 - 75
19X-RAY DIFFRACTION19( CHAIN L AND RESID 76:84 )L76 - 84
20X-RAY DIFFRACTION20( CHAIN L AND RESID 85:92 )L85 - 92
21X-RAY DIFFRACTION21( CHAIN L AND RESID 93:102 )L93 - 102
22X-RAY DIFFRACTION22( CHAIN L AND RESID 103:107 )L103 - 107
23X-RAY DIFFRACTION23( CHAIN B AND RESID 1:50 )B1 - 50
24X-RAY DIFFRACTION24( CHAIN B AND RESID 51:82 )B51 - 82
25X-RAY DIFFRACTION25( CHAIN B AND RESID 83:108 )B83 - 108
26X-RAY DIFFRACTION26( CHAIN B AND RESID 109:143 )B109 - 143
27X-RAY DIFFRACTION27( CHAIN B AND RESID 144:184 )B144 - 184
28X-RAY DIFFRACTION28( CHAIN B AND RESID 185:275 )B185 - 275
29X-RAY DIFFRACTION29( CHAIN B AND RESID 276:325 )B276 - 325
30X-RAY DIFFRACTION30( CHAIN B AND RESID 326:361 )B326 - 361
31X-RAY DIFFRACTION31( CHAIN B AND RESID 362:403 )B362 - 403
32X-RAY DIFFRACTION32( CHAIN A AND RESID 1:275 )A1 - 275
33X-RAY DIFFRACTION33( CHAIN A AND RESID 276:403 )A276 - 403
34X-RAY DIFFRACTION34( CHAIN Z AND RESID 1:50 )Z1 - 50
35X-RAY DIFFRACTION35( CHAIN Z AND RESID 51:82 )Z51 - 82
36X-RAY DIFFRACTION36( CHAIN Z AND RESID 83:278 )Z83 - 278
37X-RAY DIFFRACTION37( CHAIN Z AND RESID 279:342 )Z279 - 342
38X-RAY DIFFRACTION38( CHAIN Z AND RESID 343:403 )Z343 - 403
39X-RAY DIFFRACTION39( CHAIN E AND RESID 1:50 )E1 - 50
40X-RAY DIFFRACTION40( CHAIN E AND RESID 51:72 )E51 - 72
41X-RAY DIFFRACTION41( CHAIN E AND RESID 73:143 )E73 - 143
42X-RAY DIFFRACTION42( CHAIN E AND RESID 144:164 )E144 - 164
43X-RAY DIFFRACTION43( CHAIN E AND RESID 165:218 )E165 - 218
44X-RAY DIFFRACTION44( CHAIN E AND RESID 219:257 )E219 - 257
45X-RAY DIFFRACTION45( CHAIN E AND RESID 258:304 )E258 - 304
46X-RAY DIFFRACTION46( CHAIN E AND RESID 305:361 )E305 - 361
47X-RAY DIFFRACTION47( CHAIN E AND RESID 362:403 )E362 - 403
48X-RAY DIFFRACTION48( CHAIN F AND RESID 1:8 )F1 - 8
49X-RAY DIFFRACTION49( CHAIN F AND RESID 9:17 )F9 - 17
50X-RAY DIFFRACTION50( CHAIN F AND RESID 18:24 )F18 - 24
51X-RAY DIFFRACTION51( CHAIN F AND RESID 25:32 )F25 - 32
52X-RAY DIFFRACTION52( CHAIN F AND RESID 33:39 )F33 - 39
53X-RAY DIFFRACTION53( CHAIN F AND RESID 40:51 )F40 - 51
54X-RAY DIFFRACTION54( CHAIN F AND RESID 52:59 )F52 - 59
55X-RAY DIFFRACTION55( CHAIN F AND RESID 60:72 )F60 - 72
56X-RAY DIFFRACTION56( CHAIN F AND RESID 73:82 )F73 - 82
57X-RAY DIFFRACTION57( CHAIN F AND RESID 83:95 )F83 - 95
58X-RAY DIFFRACTION58( CHAIN F AND RESID 96:106 )F96 - 106
59X-RAY DIFFRACTION59( CHAIN F AND RESID 107:113 )F107 - 113
60X-RAY DIFFRACTION60( CHAIN G AND RESID 1:8 )G1 - 8
61X-RAY DIFFRACTION61( CHAIN G AND RESID 9:18 )G9 - 18
62X-RAY DIFFRACTION62( CHAIN G AND RESID 19:32 )G19 - 32
63X-RAY DIFFRACTION63( CHAIN G AND RESID 33:38 )G33 - 38
64X-RAY DIFFRACTION64( CHAIN G AND RESID 39:48 )G39 - 48
65X-RAY DIFFRACTION65( CHAIN G AND RESID 49:61 )G49 - 61
66X-RAY DIFFRACTION66( CHAIN G AND RESID 62:75 )G62 - 75
67X-RAY DIFFRACTION67( CHAIN G AND RESID 76:84 )G76 - 84
68X-RAY DIFFRACTION68( CHAIN G AND RESID 85:95 )G85 - 95
69X-RAY DIFFRACTION69( CHAIN G AND RESID 96:102 )G96 - 102
70X-RAY DIFFRACTION70( CHAIN G AND RESID 103:107 )G103 - 107
71X-RAY DIFFRACTION71( CHAIN I AND RESID 1:17 )I1 - 17
72X-RAY DIFFRACTION72( CHAIN I AND RESID 18:32 )I18 - 32
73X-RAY DIFFRACTION73( CHAIN I AND RESID 33:51 )I33 - 51
74X-RAY DIFFRACTION74( CHAIN I AND RESID 52:72 )I52 - 72
75X-RAY DIFFRACTION75( CHAIN I AND RESID 73:95 )I73 - 95
76X-RAY DIFFRACTION76( CHAIN I AND RESID 96:101 )I96 - 101
77X-RAY DIFFRACTION77( CHAIN I AND RESID 102:113 )I102 - 113
78X-RAY DIFFRACTION78( CHAIN J AND RESID 1:38 )J1 - 38
79X-RAY DIFFRACTION79( CHAIN J AND RESID 39:49 )J39 - 49
80X-RAY DIFFRACTION80( CHAIN J AND RESID 50:61 )J50 - 61
81X-RAY DIFFRACTION81( CHAIN J AND RESID 62:107 )J62 - 107
82X-RAY DIFFRACTION82( CHAIN M AND RESID 1:25 )M1 - 25
83X-RAY DIFFRACTION83( CHAIN M AND RESID 26:32 )M26 - 32
84X-RAY DIFFRACTION84( CHAIN M AND RESID 33:39 )M33 - 39
85X-RAY DIFFRACTION85( CHAIN M AND RESID 40:51 )M40 - 51
86X-RAY DIFFRACTION86( CHAIN M AND RESID 52:59 )M52 - 59
87X-RAY DIFFRACTION87( CHAIN M AND RESID 60:72 )M60 - 72
88X-RAY DIFFRACTION88( CHAIN M AND RESID 73:87 )M73 - 87
89X-RAY DIFFRACTION89( CHAIN M AND RESID 88:95 )M88 - 95
90X-RAY DIFFRACTION90( CHAIN M AND RESID 96:106 )M96 - 106
91X-RAY DIFFRACTION91( CHAIN M AND RESID 107:113 )M107 - 113
92X-RAY DIFFRACTION92( CHAIN N AND RESID 1:8 )N1 - 8
93X-RAY DIFFRACTION93( CHAIN N AND RESID 9:24 )N9 - 24
94X-RAY DIFFRACTION94( CHAIN N AND RESID 25:32 )N25 - 32
95X-RAY DIFFRACTION95( CHAIN N AND RESID 33:38 )N33 - 38
96X-RAY DIFFRACTION96( CHAIN N AND RESID 39:48 )N39 - 48
97X-RAY DIFFRACTION97( CHAIN N AND RESID 49:61 )N49 - 61
98X-RAY DIFFRACTION98( CHAIN N AND RESID 62:75 )N62 - 75
99X-RAY DIFFRACTION99( CHAIN N AND RESID 76:84 )N76 - 84
100X-RAY DIFFRACTION100( CHAIN N AND RESID 85:92 )N85 - 92
101X-RAY DIFFRACTION101( CHAIN N AND RESID 93:107 )N93 - 107

+
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