[English] 日本語
Yorodumi
- PDB-6wj1: Crystal structure of Fab 54-4H03 bound to H1 influenza hemagglutinin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wj1
TitleCrystal structure of Fab 54-4H03 bound to H1 influenza hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • Fab 54-4H03 heavy chain
  • Fab 54-4H03 light chain
KeywordsIMMUNE SYSTEM / Antibody / Influenza hemagglutinin
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI139445 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Convergent Evolution in Breadth of Two VH6-1-Encoded Influenza Antibody Clonotypes from a Single Donor.
Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / ...Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / McDermott, A.B. / Wilson, I.A.
History
DepositionApr 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn
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 / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 23, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first
Revision 2.2Oct 18, 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
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
D: Hemagglutinin HA2 chain
F: Hemagglutinin HA2 chain
H: Fab 54-4H03 heavy chain
L: Fab 54-4H03 light chain
J: Fab 54-4H03 heavy chain
K: Fab 54-4H03 light chain
G: Fab 54-4H03 heavy chain
I: Fab 54-4H03 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,23930
Polymers315,39112
Non-polymers6,84718
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53390 Å2
ΔGint-190 kcal/mol
Surface area119270 Å2
Unit cell
Length a, b, c (Å)231.538, 259.211, 165.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 36658.324 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3S7XTA4, UniProt: C3W5S1*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 19992.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3S5H8L7, UniProt: C3W5S1*PLUS

-
Antibody , 2 types, 6 molecules HJGLKI

#3: Antibody Fab 54-4H03 heavy chain


Mass: 24881.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Fab 54-4H03 light chain


Mass: 23598.088 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Sugars , 7 types, 18 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 11% PEG 6000 and 0.1 M MES pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 62420 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.084 / Rrim(I) all: 0.21 / Χ2: 0.861 / Net I/σ(I): 4.4 / Num. measured all: 374579
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.616.31.14356230.6780.4841.2450.47199.8
3.61-3.746.20.93556080.7210.4061.0230.56599.8
3.74-3.8960.71655950.780.3160.7860.57999.8
3.89-4.075.60.50456250.8920.2330.5570.54199.6
4.07-4.285.80.32656310.9470.1480.360.55100
4.28-4.555.80.23456550.9680.1060.2580.684100
4.55-4.96.40.1856630.9820.0770.1960.777100
4.9-5.46.20.15256820.9860.0660.1660.812100
5.4-6.175.60.13556860.9840.0620.1490.90599.7
6.17-7.786.20.10157360.990.0440.111.26399.9
7.78-505.90.05959160.9970.0260.0652.26999.7

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M4Y

4m4y


Resolution: 3.503→47.217 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 3149 5.05 %
Rwork0.1791 59210 -
obs0.1817 62359 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 390.81 Å2 / Biso mean: 124.6618 Å2 / Biso min: 47.6 Å2
Refinement stepCycle: final / Resolution: 3.503→47.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21935 0 448 0 22383
Biso mean--167.34 --
Num. residues----2820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.503-3.55760.33271560.2988257997
3.5576-3.61590.28351400.26672655100
3.6159-3.67820.29991490.27042639100
3.6782-3.74510.36861320.24442699100
3.7451-3.81710.27671250.23652662100
3.8171-3.8950.2751460.23632661100
3.895-3.97960.24241620.21042649100
3.9796-4.07220.26371430.2021266299
4.0722-4.17390.23941310.18142677100
4.1739-4.28670.23191790.16932655100
4.2867-4.41280.23991440.16172678100
4.4128-4.55510.21581340.1482711100
4.5551-4.71770.18661340.13782712100
4.7177-4.90640.18371200.14192691100
4.9064-5.12950.1951230.14472723100
5.1295-5.39960.21311510.14182688100
5.3996-5.73730.2021330.15822718100
5.7373-6.17940.2081470.17542710100
6.1794-6.79960.23161520.17792701100
6.7996-7.77980.23341540.17722731100
7.7798-9.78730.21031520.15622752100
9.7873-47.2170.22271420.1806285799
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)
11.31341.12380.22884.96150.30550.5070.08120.4180.6924-0.6517-0.2054-0.1799-0.33810.10410.09011.28240.16250.46830.95310.26681.2925-41.333713.4427-50.9377
22.61143.5138-0.94738.7853-1.30991.04930.06130.37040.0411-0.47060.2141-0.4487-0.3672-0.0367-0.2191.15660.1680.23490.93850.08721.0146-46.9192-16.0694-52.431
32.12782.50820.28247.20212.59542.6934-0.06820.5823-0.1336-0.9469-0.42590.63550.5254-0.03140.43721.11230.22580.14211.0175-0.18520.7211-61.2613-44.3084-52.8596
41.88051.82081.10169.05552.64072.29780.1670.19940.52970.0854-0.0238-0.1812-0.15350.0224-0.21360.70640.11430.23470.7404-0.00250.4941-49.7938-23.1748-40.1083
57.00990.09150.92412.56221.44716.0758-0.1811-0.0466-1.088-1.1508-0.44481.88620.8873-1.51430.52661.776-0.04810.01681.2013-0.57331.8639-71.6568-66.6296-51.9281
61.35651.21350.20646.50961.2360.63090.2541-0.17040.59470.3703-0.2031-0.4172-0.3386-0.2261-0.0221.19370.08470.15730.8429-0.03831.0914-57.359315.919-19.7839
72.25351.13641.01813.39452.03471.18160.22380.02370.56520.9055-0.2820.06980.0899-0.6232-0.03051.17640.10690.05310.8129-0.07650.8334-67.3207-10.3393-25.6098
87.36773.78610.88837.40550.40792.47640.4891-0.3395-0.402-0.3319-0.56980.35140.2857-0.61380.13560.65220.04740.08740.7774-0.09390.6406-73.8963-41.7509-25.6124
92.65042.71990.22134.33120.53490.91750.15490.0106-0.42990.2452-0.1618-0.46690.2516-0.23970.00930.6235-0.01780.11340.828-0.10640.9395-67.389-40.0815-30.2061
102.4231-0.1026-0.25665.0350.79193.07540.1861-0.60190.66360.3279-0.03750.0299-0.15160.2762-0.05110.53360.1130.21520.67680.08860.7085-50.1902-48.4162-20.1105
111.43412.5998-0.10455.4787-0.48280.14550.1085-0.08870.29530.4775-0.2745-0.8811-0.3290.24160.1711.056-0.102-0.02021.07350.00732.0033-23.71095.0198-21.7483
121.37660.63660.45536.98320.08681.85320.1346-0.1438-0.2418-0.5271-0.3343-0.12220.6226-0.05040.19920.66220.0820.12920.69870.0080.7761-44.7541-47.5761-28.1943
130.683-1.1136-0.11326.4205-1.7560.7176-0.16330.06840.0851-0.00220.2963-0.0293-0.4410.1045-0.10190.75320.07460.18540.715-0.05090.9794-49.5344-22.6831-26.9995
146.27460.80821.43268.3649-0.69814.61310.93810.3873-1.3511-1.46-0.4905-0.18190.75890.3257-0.47031.46760.0783-0.05270.8478-0.06721.5365-54.0179-72.1774-34.4446
152.5844-1.68680.88821.7058-2.19234.14090.38220.88070.2613-1.1439-0.44470.3280.57590.36060.02111.93480.3075-0.10681.6643-0.30670.9846-64.8226-41.4969-83.1932
161.72190.36721.26930.7017-1.50377.8941-0.2170.24180.2280.60690.2549-0.841.95190.1735-0.02353.02320.4269-0.19891.9155-0.3621.9544-78.9705-25.0319-107.4588
177.8088-0.46170.72250.4141-0.07861.5835-0.0154-0.7797-0.94260.34120.02480.30830.014-0.1415-0.04340.85620.08580.11190.81880.1660.8068-20.6151-61.7096-14.6577
184.77350.5042-0.11726.3185-0.16171.78580.1841-1.1097-0.19470.69610.06330.3206-0.1639-0.1068-0.23130.95220.10130.15761.02150.09750.45565.5071-55.163-10.7541
195.5746-0.01472.30163.8858-0.62226.1273-0.0564-0.12580.6787-0.5956-0.07260.3411-0.6412-1.12440.05551.71840.333-0.1721.5303-0.04441.114-74.7855-29.2186-69.89
202.06750.93870.90570.891-0.69882.86360.53080.7762-0.2613-1.34660.0182-0.2251-0.2878-1.4782-0.57512.53230.53880.00172.19680.09281.4394-94.0603-28.2058-100.3592
216.1802-0.221-1.00914.3701-1.23557.97450.27690.43930.0016-0.24030.01780.69170.0433-0.8109-0.23670.5009-0.0708-0.06740.91220.08220.6737-97.9109-40.4846-12.2539
223.0836-0.3647-2.56770.7054-0.89424.23750.0557-0.09290.47710.48290.48610.3387-1.0893-0.4592-0.51140.90570.12990.25630.892-0.00711.0011-104.7747-33.441918.6933
234.83140.94421.30914.8795-0.30244.4680.1702-0.13180.57290.396-0.2367-0.1023-0.25210.63550.0290.6303-0.17750.04850.7650.00140.6897-78.7032-34.9829-0.3308
245.86661.73220.32816.392-1.51735.50210.3468-0.83360.05950.57440.123-0.2342-0.3858-0.0443-0.42860.631-0.03210.05860.85290.03660.5258-96.5633-43.146329.7916
258.77262.0539-2.36423.3499-1.3263.38790.1390.33690.12890.302-0.22940.0739-0.2787-0.05320.09490.69530.09970.13840.62670.01810.5818-19.7763-50.8291-32.8888
264.8965-2.01831.35334.5868-1.75152.83790.0886-0.4409-0.22540.1306-0.09860.1244-0.40190.42770.10170.632-0.00520.03631.0210.10940.627716.031-57.5878-23.4034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:262)A10 - 262
2X-RAY DIFFRACTION2(chain A and resid 263:325)A263 - 325
3X-RAY DIFFRACTION3(chain B and resid 1:61)B1 - 61
4X-RAY DIFFRACTION4(chain B and resid 62:124)B62 - 124
5X-RAY DIFFRACTION5(chain B and resid 125:175)B125 - 175
6X-RAY DIFFRACTION6(chain C and resid 9:261)C9 - 261
7X-RAY DIFFRACTION7(chain C and resid 262:324)C262 - 324
8X-RAY DIFFRACTION8(chain D and resid 1:62)D1 - 62
9X-RAY DIFFRACTION9(chain D and resid 63:171)D63 - 171
10X-RAY DIFFRACTION10(chain E and resid 8:42)E8 - 42
11X-RAY DIFFRACTION11(chain E and resid 43:325)E43 - 325
12X-RAY DIFFRACTION12(chain F and resid 1:68)F1 - 68
13X-RAY DIFFRACTION13(chain F and resid 69:119)F69 - 119
14X-RAY DIFFRACTION14(chain F and resid 120:171)F120 - 171
15X-RAY DIFFRACTION15(chain G and resid 1:135)G1 - 135
16X-RAY DIFFRACTION16(chain G and resid 136:214)G136 - 214
17X-RAY DIFFRACTION17(chain H and resid 1:133)H1 - 133
18X-RAY DIFFRACTION18(chain H and resid 134:214)H134 - 214
19X-RAY DIFFRACTION19(chain I and resid 1:106)I1 - 106
20X-RAY DIFFRACTION20(chain I and resid 107:213)I107 - 213
21X-RAY DIFFRACTION21(chain J and resid 1:98)J1 - 98
22X-RAY DIFFRACTION22(chain J and resid 99:214)J99 - 214
23X-RAY DIFFRACTION23(chain K and resid 1:107)K1 - 107
24X-RAY DIFFRACTION24(chain K and resid 108:213)K108 - 213
25X-RAY DIFFRACTION25(chain L and resid 1:107)L1 - 107
26X-RAY DIFFRACTION26(chain L and resid 108:213)L108 - 213

+
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