[English] 日本語
Yorodumi
- PDB-5w6d: Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w6d
TitleCrystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and 9H/109L
Components
  • (BG505-SOSIP.v4.1-GT1-N137A ...) x 2
  • 109L FAB light chain
  • 35022 FAB heavy chain
  • 35022 FAB light chain
  • 9H FAB heavy chain
KeywordsVIRAL PROTEIN/Immune System / HIV-1 broadly neutralizing antibody / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsGarces, F. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 United States
CitationJournal: J. Exp. Med. / Year: 2017
Title: Design and crystal structure of a native-like HIV-1 envelope trimer that engages multiple broadly neutralizing antibody precursors in vivo.
Authors: Medina-Ramirez, M. / Garces, F. / Escolano, A. / Skog, P. / de Taeye, S.W. / Del Moral-Sanchez, I. / McGuire, A.T. / Yasmeen, A. / Behrens, A.J. / Ozorowski, G. / van den Kerkhof, T.L.G.M. / ...Authors: Medina-Ramirez, M. / Garces, F. / Escolano, A. / Skog, P. / de Taeye, S.W. / Del Moral-Sanchez, I. / McGuire, A.T. / Yasmeen, A. / Behrens, A.J. / Ozorowski, G. / van den Kerkhof, T.L.G.M. / Freund, N.T. / Dosenovic, P. / Hua, Y. / Gitlin, A.D. / Cupo, A. / van der Woude, P. / Golabek, M. / Sliepen, K. / Blane, T. / Kootstra, N. / van Breemen, M.J. / Pritchard, L.K. / Stanfield, R.L. / Crispin, M. / Ward, A.B. / Stamatatos, L. / Klasse, P.J. / Moore, J.P. / Nemazee, D. / Nussenzweig, M.C. / Wilson, I.A. / Sanders, R.W.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / _chem_comp.type / _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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,22718
Polymers168,3796
Non-polymers7,84712
Water00
1
G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
hetero molecules

G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
hetero molecules

G: BG505-SOSIP.v4.1-GT1-N137A gp120
B: BG505-SOSIP.v4.1-GT1-N137A gp41
L: 109L FAB light chain
H: 9H FAB heavy chain
D: 35022 FAB heavy chain
E: 35022 FAB light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,68054
Polymers505,13818
Non-polymers23,54136
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area88950 Å2
ΔGint81 kcal/mol
Surface area201920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.952, 126.952, 315.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
BG505-SOSIP.v4.1-GT1-N137A ... , 2 types, 2 molecules GB

#1: Protein BG505-SOSIP.v4.1-GT1-N137A gp120


Mass: 53350.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): 293S freestyle / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6*PLUS
#2: Protein BG505-SOSIP.v4.1-GT1-N137A gp41


Mass: 17146.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): 293S freestyle / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

-
Antibody , 4 types, 4 molecules LHDE

#3: Antibody 109L FAB light chain


Mass: 23426.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 freestyle / Production host: Homo sapiens (human)
#4: Antibody 9H FAB heavy chain


Mass: 25353.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 freestyle / Production host: Homo sapiens (human)
#5: Antibody 35022 FAB heavy chain


Mass: 25783.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 freestyle / Production host: Homo sapiens (human)
#6: Antibody 35022 FAB light chain


Mass: 23318.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 freestyle / Production host: Homo sapiens (human)

-
Sugars , 7 types, 12 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#10: 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
#11: 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
#12: 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
#13: 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.: 4
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.2M NaCl, 34% PEG 300, 0.1M NaOAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 3.2→49.433 Å / Num. obs: 47220 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 97 Å2 / CC1/2: 0.89 / Rpim(I) all: 0.077 / Rsym value: 0.174 / Χ2: 1.14 / Net I/av σ(I): 11 / Net I/σ(I): 11
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2375 / CC1/2: 0.52 / Rpim(I) all: 0.77 / Rsym value: 1 / Χ2: 1.22 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cez

5cez


Resolution: 3.202→49.433 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 2409 5.12 %
Rwork0.2424 --
obs0.2437 47083 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.202→49.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11206 0 522 0 11728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512061
X-RAY DIFFRACTIONf_angle_d0.75416511
X-RAY DIFFRACTIONf_dihedral_angle_d16.5914502
X-RAY DIFFRACTIONf_chiral_restr0.0671974
X-RAY DIFFRACTIONf_plane_restr0.0062021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2015-3.26690.4141420.41022636X-RAY DIFFRACTION100
3.2669-3.33790.46461590.37832615X-RAY DIFFRACTION100
3.3379-3.41550.39781490.37722582X-RAY DIFFRACTION100
3.4155-3.50090.41811430.34852611X-RAY DIFFRACTION100
3.5009-3.59550.35821360.34122625X-RAY DIFFRACTION100
3.5955-3.70130.34081550.30982596X-RAY DIFFRACTION100
3.7013-3.82070.37171320.30942638X-RAY DIFFRACTION100
3.8207-3.95720.33871160.28832673X-RAY DIFFRACTION100
3.9572-4.11560.30161300.27122616X-RAY DIFFRACTION100
4.1156-4.30280.24041270.24562653X-RAY DIFFRACTION100
4.3028-4.52950.24631660.21622609X-RAY DIFFRACTION100
4.5295-4.81310.25641360.20632607X-RAY DIFFRACTION100
4.8131-5.18440.19551410.19932635X-RAY DIFFRACTION100
5.1844-5.70540.23841460.21562645X-RAY DIFFRACTION100
5.7054-6.52940.25341330.23742630X-RAY DIFFRACTION100
6.5294-8.22020.25781360.21512663X-RAY DIFFRACTION100
8.2202-49.43850.1951620.17982640X-RAY DIFFRACTION99
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)
10.350.1566-0.47030.4333-0.97845.39890.00030.2176-0.1457-0.0811-0.1205-0.039-0.12820.2775-0.11350.6772-0.0570.08730.73380.0540.80781.333828.4772131.5457
21.00670.3273-0.63790.623-0.67673.6953-0.1254-0.0614-0.1748-0.1561-0.2016-0.23680.49830.72910.10580.74750.1450.16710.73360.10240.905192.623319.6977132.6811
30.1719-0.7172-0.04576.3076-4.07324.41330.08050.14090.13631.2548-0.9337-0.3482-0.56981.36960.53390.6844-0.31940.02461.07150.07980.714182.912927.4225170.4268
42.87191.5803-0.40953.85850.41780.19681.23271.30230.1719-0.7049-0.5685-0.5158-0.359-1.0042-0.46911.43840.67910.20071.53650.2130.904170.581340.435143.2157
54.87990.5029-2.13315.1332-2.7262.6670.4886-0.2604-0.5252-1.0263-0.264-0.06361.04840.8161-0.06170.54170.1149-0.06151.03610.0110.726867.437531.2253156.3613
60.1783-0.7108-0.47133.31292.56662.04260.2873-0.820.94871.30.13660.4975-0.7573-0.1101-0.16310.69850.34210.20481.4942-0.13740.787164.008828.4953175.3566
77.52332.9807-4.02645.6693-2.70973.8342-0.6391-1.1084-0.4356-0.00391.20211.53651.6383-1.07060.20181.1438-0.32-0.04231.41810.16610.896767.473717.3925179.9326
86.92491.5798-1.85016.95861.53185.1028-0.61830.4157-1.41040.53890.067-0.00881.85310.2992-0.08820.9003-0.0380.2720.69070.12330.911377.192311.8494174.8723
93.67880.4796-0.29197.0275-0.90683.38120.24040.5111-0.71540.03360.05411.75890.777-0.94220.41280.6699-0.79060.06972.28750.24530.928560.255317.7076174.1063
104.89313.16050.83722.5142-1.1867.25811.94990.31140.31060.2401-0.01260.82290.1563-0.7844-0.6322.15280.53550.22843.22040.561.332150.856729.3466185.6607
113.0704-1.5909-1.63512.6064-1.52235.20041.1129-0.8518-0.09830.3655-0.2092-0.0553-0.4163-0.5396-0.17671.3844-0.1420.07481.20970.09631.2047114.942454.389188.1774
121.91550.6933-2.41720.2865-0.91423.05240.66120.53591.2377-1.10040.0023-0.16570.36660.856-0.86190.96970.3474-0.00781.4259-0.05930.9489108.070340.177497.9158
130.5002-0.28780.85180.84120.13141.99250.20860.51280.1265-1.16740.0485-0.1706-0.1585-0.2184-0.46031.0812-0.11320.29381.08480.06880.9698122.072742.058286.6234
144.6403-1.1686-1.74928.11721.3991.1008-1.1401-0.41460.20510.11370.5106-0.44850.4741-0.34780.18090.962-0.2990.03611.0899-0.05580.871119.965343.4745100.5807
154.019-0.5879-2.66981.7304-2.04336.8065-0.1266-0.43880.2952-0.2387-0.0160.21-0.16861.57520.05050.6158-0.17180.11130.7108-0.04970.9447120.2949.397589.5146
162.3333-0.5502-1.58640.20630.67523.0203-0.38990.25210.30140.38590.5403-0.3641-0.39690.33010.12210.7474-0.07170.22781.04750.1161.1074108.558434.166792.5929
171.641.4932-1.4311.11-1.23021.79450.3669-0.67030.51520.352-0.488-0.23630.3490.93090.40.8433-0.0279-0.11651.02630.15040.9955126.117759.523374.2491
189.45421.2567-0.06516.47010.16694.93560.26770.3419-0.6279-0.56920.5845-0.36970.36550.103-0.58091.62020.10730.29171.37280.20491.398133.925948.830744.8343
195.1125-0.5624-3.18212.29081.61173.0525-0.4558-0.21060.4146-0.4348-0.20610.1478-0.37450.99050.78770.94450.03980.13860.89090.08471.0229126.402259.680861.7296
204.90140.8161-0.99744.1851.08975.6839-1.3448-0.01730.3988-0.7105-0.465-0.0272-0.41511.32510.53380.7411-0.21840.10480.85050.00381.1982124.064257.320262.191
215.4730.34860.79265.39132.10155.3504-0.24031.0143-0.0423-2.10420.40891.0162-0.1471.4548-0.4611.3986-0.0896-0.01151.19240.02381.3106127.302155.658550.3798
221.82461.0898-0.32122.1692-0.59984.5374-0.1920.6839-0.311-0.43090.12641.1819-0.3048-0.6806-0.18341.2433-0.15690.16560.93250.08331.2622129.087465.517755.4233
230.9217-1.3362-0.32812.2582-0.99242.6515-0.3853-0.1707-0.5580.0792-0.2604-0.14870.89870.01010.2431.8689-0.15270.51971.14520.02671.1941123.88827.533871.3897
242.20970.33510.94490.1829-0.58313.0584-0.0339-0.523-1.3923-0.63840.1352-0.61180.34681.23780.15090.79760.40670.27771.44370.32251.5024127.914922.480582.2381
255.86830.6209-0.83354.47990.28215.9337-0.1207-0.00460.0715-0.6126-0.460.08231.74870.50620.1751.20660.09610.11110.74830.15990.9841116.739830.940681.3246
260.6846-0.36451.35878.60490.65443.3731-1.8421-0.876-0.78441.29880.79420.21311.99750.11320.1691.6404-0.06260.45590.99830.20831.1442114.340620.379882.0973
273.33372.22360.45763.01751.93923.5836-0.70480.4795-0.94810.22160.67490.13450.7340.6297-0.19611.07830.05030.46910.67170.09811.1835120.708426.076277.0225
280.5558-0.3024-0.91842.4315-1.00264.65920.2627-0.0546-0.3755-0.00770.2979-0.14370.00010.2146-0.20231.12510.02380.23971.34320.19971.025114.747428.0214100.4927
291.98562.2264-0.87644.3096-1.22392.7072-0.1264-0.68920.0432-0.70640.0206-0.29960.77490.1736-0.09571.12760.28150.33641.06940.02611.1786132.17343.946359.3817
304.28120.75880.1043.01381.81513.636-0.2990.38720.336-0.30830.4119-0.43760.76081.03050.01091.33090.04120.19061.39690.27091.2227135.148342.558263.2926
315.3337-0.2439-0.42584.09020.99461.26430.2319-0.2318-0.74560.3603-0.0083-0.96190.38080.34230.11980.9306-0.00370.27871.1829-0.02941.1738136.632946.980359.9146
325.42582.8194-0.43114.4531-0.63950.6046-1.13810.3983-0.61160.09810.0797-0.73642.08380.09890.81511.6771-0.09820.90271.5909-0.29991.8741139.183139.700255.0987
338.7037-3.52663.45224.2494-1.04772.73790.75170.20560.27-0.2948-0.03140.02630.2479-0.4362-0.4131.25950.0689-0.02270.95340.32771.1485106.4627-7.3307175.0535
340.93220.5997-0.06422.74390.29312.46330.14170.32030.0699-0.0588-0.1273-0.27180.37250.6466-0.11130.86220.1610.10661.12090.31141.0317102.1492.6887178.2865
351.2886-1.72080.89523.1054-0.23583.02590.46981.0992-0.66080.59450.9853-0.92631.2821-0.9194-0.86981.83960.27190.37982.0449-0.10251.7382107.1141-30.049177.1745
364.31344.11322.23954.07872.09971.81620.23020.8819-0.40180.224-0.73710.29390.952-1.0718-0.70791.8840.41610.30391.5652-0.15641.8896101.7734-28.0354177.3389
370.65421.3254-0.62086.34331.01242.1758-0.17650.9626-0.6894-0.18390.69641.15611.03911.2788-0.93851.83910.34960.17611.4638-0.18351.9049100.2532-26.4316180.1725
381.59053.08091.55976.87023.17331.6070.44192.2365-0.9111-1.5355-0.61030.67230.762-0.9835-0.8432.1742-0.2298-0.37522.3771-1.15852.057789.4981-36.1971173.3838
393.1974-0.6073.06543.077-3.03334.9998-1.69010.5645-0.4658-0.6411-1.6511.4673-0.9301-2.47662.00861.62160.61660.18482.8081-0.87732.1806103.6053-27.1599168.828
402.80072.02631.06145.47830.60221.00960.0451-0.7185-0.22961.4982-0.28380.36720.19380.38720.39691.70730.14670.2241.40.17681.408290.5624-5.2676202.7804
413.10890.31960.48992.4847-0.98992.5881-0.5291-0.4496-0.31390.55960.29570.23260.2198-0.2590.33391.49450.22790.19541.3030.31681.171190.1670.9965194.8075
421.1579-0.0591-0.22256.72171.18061.38430.1394-0.1541-0.80271.7893-1.16551.1693-0.5234-0.4120.49912.67990.34630.62821.160.50471.883385.3662-21.6718199.1637
431.28851.50880.24132.6768-0.88581.67450.40111.0385-0.1255-0.0231-0.386-0.9471-0.70420.6386-0.34272.1562-0.09290.30041.67360.04622.4303105.574-40.8265181.5126
440.36760.0639-0.49920.10130.00891.69320.5234-0.6264-0.81691.13730.26040.027-0.59460.2722-0.04022.14480.29760.05141.56820.38152.116997.7846-33.0242193.5726
450.61771.2912-0.52473.0159-0.62852.61260.19880.0863-0.88010.6717-0.9075-0.45410.90310.46490.07732.09210.185-0.00791.67050.00962.270199.8929-30.6098193.5797
461.5074-0.0856-0.27960.0146-0.21612.77691.305-0.5274-0.1937-0.27241.00761.2545-1.32140.2859-0.60441.68420.38450.38721.40220.1652.4948106.995-38.3886188.832
473.08991.20950.23351.1172-1.23242.9221.0605-0.5159-1.13630.0366-0.3991-0.07880.26750.6863-0.58032.6683-0.00210.35331.46560.30893.047898.971-43.059194.695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 32 through 235 )
2X-RAY DIFFRACTION2chain 'G' and (resid 236 through 506 )
3X-RAY DIFFRACTION3chain 'B' and (resid 518 through 544 )
4X-RAY DIFFRACTION4chain 'B' and (resid 545 through 569 )
5X-RAY DIFFRACTION5chain 'B' and (resid 570 through 595 )
6X-RAY DIFFRACTION6chain 'B' and (resid 596 through 600 )
7X-RAY DIFFRACTION7chain 'B' and (resid 601 through 615 )
8X-RAY DIFFRACTION8chain 'B' and (resid 616 through 638 )
9X-RAY DIFFRACTION9chain 'B' and (resid 639 through 650 )
10X-RAY DIFFRACTION10chain 'B' and (resid 651 through 664 )
11X-RAY DIFFRACTION11chain 'L' and (resid 6 through 22 )
12X-RAY DIFFRACTION12chain 'L' and (resid 23 through 33 )
13X-RAY DIFFRACTION13chain 'L' and (resid 34 through 48 )
14X-RAY DIFFRACTION14chain 'L' and (resid 49 through 71 )
15X-RAY DIFFRACTION15chain 'L' and (resid 72 through 89 )
16X-RAY DIFFRACTION16chain 'L' and (resid 90 through 101 )
17X-RAY DIFFRACTION17chain 'L' and (resid 102 through 119 )
18X-RAY DIFFRACTION18chain 'L' and (resid 120 through 130 )
19X-RAY DIFFRACTION19chain 'L' and (resid 131 through 151 )
20X-RAY DIFFRACTION20chain 'L' and (resid 152 through 172 )
21X-RAY DIFFRACTION21chain 'L' and (resid 173 through 188 )
22X-RAY DIFFRACTION22chain 'L' and (resid 189 through 210 )
23X-RAY DIFFRACTION23chain 'H' and (resid 1 through 17 )
24X-RAY DIFFRACTION24chain 'H' and (resid 18 through 32 )
25X-RAY DIFFRACTION25chain 'H' and (resid 33 through 51 )
26X-RAY DIFFRACTION26chain 'H' and (resid 52 through 72 )
27X-RAY DIFFRACTION27chain 'H' and (resid 73 through 96 )
28X-RAY DIFFRACTION28chain 'H' and (resid 97 through 101 )
29X-RAY DIFFRACTION29chain 'H' and (resid 102 through 140 )
30X-RAY DIFFRACTION30chain 'H' and (resid 141 through 163 )
31X-RAY DIFFRACTION31chain 'H' and (resid 164 through 198 )
32X-RAY DIFFRACTION32chain 'H' and (resid 199 through 213 )
33X-RAY DIFFRACTION33chain 'D' and (resid 1 through 17 )
34X-RAY DIFFRACTION34chain 'D' and (resid 18 through 111 )
35X-RAY DIFFRACTION35chain 'D' and (resid 112 through 134 )
36X-RAY DIFFRACTION36chain 'D' and (resid 135 through 154 )
37X-RAY DIFFRACTION37chain 'D' and (resid 155 through 177 )
38X-RAY DIFFRACTION38chain 'D' and (resid 178 through 194 )
39X-RAY DIFFRACTION39chain 'D' and (resid 195 through 211 )
40X-RAY DIFFRACTION40chain 'E' and (resid 2 through 24 )
41X-RAY DIFFRACTION41chain 'E' and (resid 25 through 105 )
42X-RAY DIFFRACTION42chain 'E' and (resid 106 through 117 )
43X-RAY DIFFRACTION43chain 'E' and (resid 118 through 133 )
44X-RAY DIFFRACTION44chain 'E' and (resid 134 through 154 )
45X-RAY DIFFRACTION45chain 'E' and (resid 155 through 175 )
46X-RAY DIFFRACTION46chain 'E' and (resid 176 through 190 )
47X-RAY DIFFRACTION47chain 'E' and (resid 191 through 214 )

+
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://pdbjlvh1.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