[English] 日本語
Yorodumi
- PDB-3ngb: Crystal structure of broadly and potently neutralizing antibody V... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ngb
TitleCrystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120
Components
  • (Antigen binding fragment of ...) x 2
  • Envelope glycoprotein gp160
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / antibody / VRC01 / neutralization / vaccine / envelope glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZhou, T. / Kwong, P.D.
CitationJournal: Science / Year: 2010
Title: Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01.
Authors: Zhou, T. / Georgiev, I. / Wu, X. / Yang, Z.Y. / Dai, K. / Finzi, A. / Do Kwon, Y. / Scheid, J.F. / Shi, W. / Xu, L. / Yang, Y. / Zhu, J. / Nussenzweig, M.C. / Sodroski, J. / Shapiro, L. / ...Authors: Zhou, T. / Georgiev, I. / Wu, X. / Yang, Z.Y. / Dai, K. / Finzi, A. / Do Kwon, Y. / Scheid, J.F. / Shi, W. / Xu, L. / Yang, Y. / Zhu, J. / Nussenzweig, M.C. / Sodroski, J. / Shapiro, L. / Nabel, G.J. / Mascola, J.R. / Kwong, P.D.
History
DepositionJun 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls_group / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Mar 31, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 3.2Sep 6, 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 3.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Envelope glycoprotein gp160
H: Antigen binding fragment of heavy chain: Antibody VRC01
L: Antigen binding fragment of light chain: Antibody VRC01
A: Envelope glycoprotein gp160
B: Antigen binding fragment of heavy chain: Antibody VRC01
C: Antigen binding fragment of light chain: Antibody VRC01
D: Envelope glycoprotein gp160
E: Antigen binding fragment of heavy chain: Antibody VRC01
F: Antigen binding fragment of light chain: Antibody VRC01
I: Envelope glycoprotein gp160
J: Antigen binding fragment of heavy chain: Antibody VRC01
K: Antigen binding fragment of light chain: Antibody VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,53682
Polymers347,00712
Non-polymers16,52970
Water9,422523
1
G: Envelope glycoprotein gp160
H: Antigen binding fragment of heavy chain: Antibody VRC01
L: Antigen binding fragment of light chain: Antibody VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,27616
Polymers86,7523
Non-polymers3,52413
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Envelope glycoprotein gp160
B: Antigen binding fragment of heavy chain: Antibody VRC01
C: Antigen binding fragment of light chain: Antibody VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,82225
Polymers86,7523
Non-polymers5,07122
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Envelope glycoprotein gp160
E: Antigen binding fragment of heavy chain: Antibody VRC01
F: Antigen binding fragment of light chain: Antibody VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,43520
Polymers86,7523
Non-polymers3,68317
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Envelope glycoprotein gp160
J: Antigen binding fragment of heavy chain: Antibody VRC01
K: Antigen binding fragment of light chain: Antibody VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,00321
Polymers86,7523
Non-polymers4,25118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.630, 98.275, 205.256
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules GADI

#1: Protein
Envelope glycoprotein gp160


Mass: 39211.434 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 43-122, 201-303, 325-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Description: HIV-1 gp120 with leader sequence / Gene: Env, pol / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31

-
Antibody , 2 types, 8 molecules HBEJLCFK

#2: Antibody
Antigen binding fragment of heavy chain: Antibody VRC01


Mass: 24367.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Codon-optimized human antibody heavy chain of VRC01
Gene: Heavy chain / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody
Antigen binding fragment of light chain: Antibody VRC01


Mass: 23172.686 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Codon-optimized human antibody light chain of VRC01
Gene: Light chain / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

-
Sugars , 4 types, 63 molecules

#4: 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.: 3
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
#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.: 1
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: 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.: 46
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
#7: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 530 molecules

#8: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 4000, 9% Isopropanol, 0.1M Ammonium Sulfate, 0.1M Tris/Cl-, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.82656 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 97150 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Redundancy: 3.4 % / Rsym value: 0.08 / Net I/σ(I): 18.6

-
Processing

Software
NameVersionClassification
APSSER-CAT MARCCDdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IDX

3idx


Resolution: 2.68→49.733 Å / SU ML: 0.36 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 4867 5.01 %RANDOM
Rwork0.1967 ---
obs0.1997 97150 94.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.594 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.981 Å2-0 Å25.7775 Å2
2--2.2145 Å20 Å2
3----5.1954 Å2
Refinement stepCycle: LAST / Resolution: 2.68→49.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24218 0 1067 523 25808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225953
X-RAY DIFFRACTIONf_angle_d0.53435243
X-RAY DIFFRACTIONf_dihedral_angle_d14.6539716
X-RAY DIFFRACTIONf_chiral_restr0.0344058
X-RAY DIFFRACTIONf_plane_restr0.0034423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.71340.3373110.3116270X-RAY DIFFRACTION7
2.7134-2.74530.251190.3339530X-RAY DIFFRACTION14
2.7453-2.77880.4039400.3578803X-RAY DIFFRACTION21
2.7788-2.8140.4475630.34381127X-RAY DIFFRACTION30
2.814-2.8510.4184660.36061551X-RAY DIFFRACTION41
2.851-2.89010.3776960.33151957X-RAY DIFFRACTION52
2.8901-2.93130.4131980.33972367X-RAY DIFFRACTION62
2.9313-2.97510.36731570.32442655X-RAY DIFFRACTION72
2.9751-3.02160.37331590.30492937X-RAY DIFFRACTION78
3.0216-3.07110.34641710.29883246X-RAY DIFFRACTION85
3.0711-3.12410.35722070.28683422X-RAY DIFFRACTION92
3.1241-3.18090.36841840.28273579X-RAY DIFFRACTION95
3.1809-3.2420.33671970.27043642X-RAY DIFFRACTION98
3.242-3.30820.31751750.26013714X-RAY DIFFRACTION98
3.3082-3.38010.31941950.23853755X-RAY DIFFRACTION99
3.3801-3.45870.29611890.22453745X-RAY DIFFRACTION99
3.4587-3.54520.2561840.21133776X-RAY DIFFRACTION99
3.5452-3.6410.27511730.19413786X-RAY DIFFRACTION100
3.641-3.74810.26171940.18963795X-RAY DIFFRACTION100
3.7481-3.8690.23122110.18173745X-RAY DIFFRACTION100
3.869-4.00730.24922280.16933744X-RAY DIFFRACTION100
4.0073-4.16760.2452060.16063750X-RAY DIFFRACTION100
4.1676-4.35720.21621900.14533793X-RAY DIFFRACTION100
4.3572-4.58680.20371860.14353799X-RAY DIFFRACTION100
4.5868-4.87390.20532210.13723773X-RAY DIFFRACTION100
4.8739-5.24990.2142060.1313765X-RAY DIFFRACTION100
5.2499-5.77750.21131870.14643830X-RAY DIFFRACTION100
5.7775-6.61180.23362270.16093785X-RAY DIFFRACTION100
6.6118-8.32390.24092130.17153817X-RAY DIFFRACTION99
8.3239-49.74120.22262140.20823825X-RAY DIFFRACTION98
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)
13.08570.7872-1.1082.8459-1.20513.00460.0861-0.11160.58720.1304-0.1021-0.5005-0.30450.0621-0.15251.0422-0.02080.1817-0.12960.080.823-31.019351.4471-96.6077
23.4581-1.0457-1.18032.6738-0.6781.6460.08930.3448-0.1311-0.59610.009-0.24850.0833-0.340701.1008-0.01390.34460.175-0.02350.607-34.553929.5912-103.2689
30.8019-0.6043-0.99991.5489-1.83592.0410.1282-0.2490.22110.08160.22260.02680.0719-0.0171-00.6952-0.0420.05180.27190.04290.621-37.132619.4353-76.2948
40.3035-0.7547-0.00462.1680.89691.720.08720.0437-0.4516-0.23690.1648-0.20450.03460.1505-00.5321-0.1313-0.0810.61920.32030.563-24.1239-14.6427-56.7231
50.9312-0.66530.92890.5201-0.84451.09450.4163-0.42870.19930.4495-0.5212-1.1645-0.13560.5057-0.00010.7077-0.0973-0.12520.61610.17221.0884-17.256422.4751-66.0029
63.0572-1.60462.40932.3241-1.89581.9591-0.12550.84-0.0283-0.3489-0.137-1.0078-0.57491.07740.00010.6119-0.25610.17590.79730.16140.9515-11.0507-6.902-61.4243
71.45610.15990.37211.6957-0.98412.517-0.1317-0.02550.1788-0.01360.40970.2637-0.5838-0.611100.37930.0508-0.12330.48820.09820.3888-48.825866.4734-42.3619
82.98560.0822-1.21391.43780.64983.04050.1290.0582-0.3588-0.3058-0.01650.09450.3074-0.3201-00.5364-0.0903-0.19190.4720.05810.5483-41.184544.5264-43.7233
92.5718-0.84171.18090.8275-0.99241.67160.0315-0.6999-0.54560.04980.49340.0583-0.1362-0.2202-0.00010.37860.0184-0.06480.56170.14870.6365-17.521149.3102-27.4529
100.01890.19350.23241.17221.21521.0721-0.5089-0.34350.04530.37190.1864-0.14070.5604-0.3635-00.83510.2648-0.11660.98490.03860.896921.711937.1324-29.3911
113.01790.4642-1.42512.0594-0.0681.31770.14430.55940.2799-0.0453-0.0777-0.8662-0.37070.1337-00.3899-0.0306-0.13060.6480.03910.7359-4.446463.5072-38.7127
122.5281-1.14890.21620.552-0.37761.31640.17680.78130.6497-0.5948-0.4449-0.5740.64090.62-0.00010.83770.24870.02911.00140.01810.789819.422246.0887-42.2084
131.36021.3743-0.05841.8912-1.24082.37290.143-0.54710.23050.4930.13630.3668-0.4447-0.0501-00.90350.19610.10370.78380.19430.5029-67.48086.0249-44.3832
142.41440.31850.15222.3944-0.95531.27890.00740.0749-0.1707-0.28820.27390.23110.2929-0.24800.7374-0.0593-0.02830.62010.21920.4609-70.422-0.1361-66.6403
152.9003-0.6019-0.54734.9863-2.67191.9333-0.2604-0.33540.142-0.29160.19560.426-0.19430.0294-0.00050.57820.20390.15970.37690.15160.2482-64.595926.2924-77.1733
16-0.02420.11740.09381.04220.64230.27731.10070.3978-0.1933-0.9388-0.29870.82810.28990.134801.77950.3785-0.29792.14110.5811.3968-83.361348.7572-107.0718
171.5097-0.65190.88042.32630.58530.84270.0709-0.75050.18330.21910.35811.5148-0.8738-0.706701.04590.51750.36471.02890.34141.1922-80.380440.5358-69.7038
180.6052-0.34610.56230.0783-0.09090.17170.00320.6290.21640.01180.29420.0164-1.0749-1.00401.0940.2939-0.23061.97850.20241.1698-93.164246.3386-94.7239
192.9328-1.08511.01132.3159-1.30882.28690.1097-1.0013-0.21550.14180.018-0.4025-0.38060.042200.259-0.1685-0.19341.24790.23490.7139-0.119643.577814.9745
201.20061.2794-0.46951.1441-0.54681.74450.326-0.5924-0.6787-0.2593-0.1502-0.33440.20740.0718-0.00010.41370.0159-0.2590.99630.50041.1358-12.381626.64834.6902
214.3798-0.5291-0.68440.8593-0.72841.8990.2336-0.2432-0.16310.03-0.33670.4047-0.31430.2533-00.39370.0869-0.01870.88390.0230.3929-33.075944.7173-4.8552
220.61430.7575-0.13192.8066-0.04880.60620.4442-0.78960.0626-0.5604-0.2349-0.04090.3894-0.15250.00010.66820.1241-0.07481.350.2760.8794-73.657440.1733-5.3249
232.36550.0218-2.28631.4968-0.09022.01090.6862-0.88950.04850.4634-0.92450.3877-0.52040.3390.00010.5479-0.22610.11511.2229-0.14420.3592-43.427253.588313.005
241.03320.683-0.65330.7557-0.11880.24020.1958-1.0107-0.04350.2337-0.2118-0.25120.34040.254800.76490.0207-0.14991.13220.14210.6736-68.749940.74789.7178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:253 OR RESID 476:492 ) )G44 - 253
2X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:253 OR RESID 476:492 ) )G476 - 492
3X-RAY DIFFRACTION2( CHAIN G AND RESID 254:475 )G254 - 475
4X-RAY DIFFRACTION3( CHAIN H AND RESID 1:121 )H1 - 121
5X-RAY DIFFRACTION4( CHAIN H AND RESID 122:216 )H122 - 216
6X-RAY DIFFRACTION5( CHAIN L AND RESID 3:103 )L3 - 103
7X-RAY DIFFRACTION6( CHAIN L AND RESID 104:208 )L104 - 208
8X-RAY DIFFRACTION7( CHAIN A AND ( RESID 44:253 OR RESID 476:492 ) )A44 - 253
9X-RAY DIFFRACTION7( CHAIN A AND ( RESID 44:253 OR RESID 476:492 ) )A476 - 492
10X-RAY DIFFRACTION8( CHAIN A AND RESID 254:475 )A254 - 475
11X-RAY DIFFRACTION9( CHAIN B AND RESID 1:121 )B1 - 121
12X-RAY DIFFRACTION10( CHAIN B AND RESID 122:216 )B122 - 216
13X-RAY DIFFRACTION11( CHAIN C AND RESID 1:103 )C1 - 103
14X-RAY DIFFRACTION12( CHAIN C AND RESID 104:208 )C104 - 208
15X-RAY DIFFRACTION13( CHAIN D AND ( RESID 44:253 OR RESID 476:492 ) )D44 - 253
16X-RAY DIFFRACTION13( CHAIN D AND ( RESID 44:253 OR RESID 476:492 ) )D476 - 492
17X-RAY DIFFRACTION14( CHAIN D AND RESID 254:475 )D254 - 475
18X-RAY DIFFRACTION15( CHAIN E AND RESID 1:121 )E1 - 121
19X-RAY DIFFRACTION16( CHAIN E AND RESID 122:216 )E122 - 216
20X-RAY DIFFRACTION17( CHAIN F AND RESID 3:103 )F3 - 103
21X-RAY DIFFRACTION18( CHAIN F AND RESID 104:208 )F104 - 208
22X-RAY DIFFRACTION19( CHAIN I AND ( RESID 44:253 OR RESID 476:492 ) )I44 - 253
23X-RAY DIFFRACTION19( CHAIN I AND ( RESID 44:253 OR RESID 476:492 ) )I476 - 492
24X-RAY DIFFRACTION20( CHAIN I AND RESID 254:475 )I254 - 475
25X-RAY DIFFRACTION21( CHAIN J AND RESID 1:121 )J1 - 121
26X-RAY DIFFRACTION22( CHAIN J AND RESID 122:216 )J122 - 216
27X-RAY DIFFRACTION23( CHAIN K AND RESID 1:103 )K1 - 103
28X-RAY DIFFRACTION24( CHAIN K AND RESID 104:208 )K104 - 208

+
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