[English] 日本語
Yorodumi
- PDB-4zmj: Crystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zmj
TitleCrystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer
Components(Envelope glycoprotein gp160) x 2
KeywordsVIRAL PROTEIN / HIV-1 / Env trimer / unliganded / BG505 SOSIP
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 / apoptotic process / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsKwon, Y.D. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.
Authors: Do Kwon, Y. / Pancera, M. / Acharya, P. / Georgiev, I.S. / Crooks, E.T. / Gorman, J. / Joyce, M.G. / Guttman, M. / Ma, X. / Narpala, S. / Soto, C. / Terry, D.S. / Yang, Y. / Zhou, T. / ...Authors: Do Kwon, Y. / Pancera, M. / Acharya, P. / Georgiev, I.S. / Crooks, E.T. / Gorman, J. / Joyce, M.G. / Guttman, M. / Ma, X. / Narpala, S. / Soto, C. / Terry, D.S. / Yang, Y. / Zhou, T. / Ahlsen, G. / Bailer, R.T. / Chambers, M. / Chuang, G.Y. / Doria-Rose, N.A. / Druz, A. / Hallen, M.A. / Harned, A. / Kirys, T. / Louder, M.K. / O'Dell, S. / Ofek, G. / Osawa, K. / Prabhakaran, M. / Sastry, M. / Stewart-Jones, G.B. / Stuckey, J. / Thomas, P.V. / Tittley, T. / Williams, C. / Zhang, B. / Zhao, H. / Zhou, Z. / Donald, B.R. / Lee, L.K. / Zolla-Pazner, S. / Baxa, U. / Schon, A. / Freire, E. / Shapiro, L. / Lee, K.K. / Arthos, J. / Munro, J.B. / Blanchard, S.C. / Mothes, W. / Binley, J.M. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 27, 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
Revision 2.2Oct 16, 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
B: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,45120
Polymers71,2112
Non-polymers5,24018
Water00
1
G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules

G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules

G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,35260
Polymers213,6326
Non-polymers15,72054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area44090 Å2
ΔGint81 kcal/mol
Surface area82270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.180, 107.180, 103.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Envelope glycoprotein gp160


Mass: 54064.277 Da / Num. of mol.: 1 / Mutation: T332N, A501C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pVRC8400 / Cell (production host): HEK293 GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein Envelope glycoprotein gp160


Mass: 17146.482 Da / Num. of mol.: 1 / Mutation: I559P, T605C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pVRC8400 / Cell (production host): HEK293 GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 2
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
#5: 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.: 15
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 26% PEG 400, 3.2% PEG 3350, and 0.1M sodium acetate pH 5.5
PH range: 5.5-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.31→50 Å / Num. all: 7041 / Num. obs: 7041 / % possible obs: 68.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 88.6 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.073 / Net I/σ(I): 18.5
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.16 / % possible all: 11.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVP

4tvp


Resolution: 3.31→35.083 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 36.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 323 5.02 %
Rwork0.2664 --
obs0.2676 6434 63.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→35.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 338 0 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044983
X-RAY DIFFRACTIONf_angle_d1.1666790
X-RAY DIFFRACTIONf_dihedral_angle_d12.8371245
X-RAY DIFFRACTIONf_chiral_restr0.047831
X-RAY DIFFRACTIONf_plane_restr0.004842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3097-3.64240.376730.3558250X-RAY DIFFRACTION10
3.6424-4.16880.2937540.29831153X-RAY DIFFRACTION48
4.1688-5.24940.30581290.29172286X-RAY DIFFRACTION96
5.2494-35.08480.26871370.23812422X-RAY DIFFRACTION100
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)
11.7995-0.77960.34981.41881.34492.1112-0.02680.57150.9827-0.4998-0.2497-0.4866-0.71630.5125-0.07630.1412-0.75520.0536-0.61520.47120.162214.983110.979620.6844
20.2816-0.0281-0.2158-0.0110.01120.29970.13460.2029-0.0761-0.17530.1749-0.2599-0.20230.05860.1604-0.03350.59510.37310.0391-0.18270.29916.8138113.9047-23.9766
30.33320.0565-0.08450.04230.00730.0313-0.01210.5562-0.045-0.24470.0606-0.093-0.0402-0.19040.180.279-0.05180.4913-0.39070.3737-0.176916.9804109.68955.6335
40.02850.0191-0.0730.0865-0.07760.39430.0023-0.0750.09910.09860.1875-0.18930.47120.08610.5150.4405-0.10250.515-0.04580.5464-0.314627.3235101.7652.4135
50.13410.0258-0.08730.11790.18520.39590.288-0.0493-0.10740.24510.05120.0450.36460.02820.6892-0.21810.12440.4747-0.86440.0485-0.423624.85996.4834-3.5996
60.1326-0.11330.01260.5631-0.06810.174-0.0154-0.2031-0.10250.3395-0.0156-0.0748-0.06580.0270.27210.4075-0.19020.152-0.02110.14030.319710.3283104.699230.9633
70.0084-0.0041-0.02180.03330.02030.0532-0.0199-0.00080.03240.0264-0.0040.005-0.00970.0655-0.00430.72880.1185-0.08670.9668-0.26790.335518.0459108.293637.0419
80.0060.0064-0.00440.0132-0.0180.02250.023-0.00610.0531-0.03320.0322-0.03090.0053-0.01760.00340.91540.0130.1781.04990.03430.381315.6722103.2545.9796
90.0194-0.00310.01920.00220.00090.03520.0080.0063-0.0447-0.02590.0534-0.0160.05930.00870.01721.0164-0.27910.06990.7473-0.3420.632414.436114.417240.1517
100.09170.00440.0851-0.0004-0.01240.41740.09190.15470.0125-0.0795-0.0223-0.03620.01480.02310.10310.45420.47490.08250.2626-0.10960.02559.4672121.439318.0453
110.00020.0017-0.01040.0934-0.03590.05260.0958-0.08120.0228-0.142-0.16060.08820.13840.0026-0.0520.53540.07820.0510.378-0.00120.19261.6112117.159530.086
120.00120.00340.00240.0250.01830.0151-0.05130.0109-0.0733-0.0157-0.02990.0451-0.0544-0.0569-0.06650.2947-0.30430.26620.8160.01350.50091.7196114.340348.1038
130.00220.00310.00090.00350.00290.0037-0.081-0.0908-0.0630.09990.0036-0.0096-0.1119-0.073801.2164-0.43240.22671.0090.21161.0983-3.293198.962951.5357
14-0.0004-0.00020.0010.0012-0.00340.00650.06890.0286-0.0122-0.03460.0806-0.02780.0664-0.0555-01.2269-0.39750.22631.4840.56581.099710.104195.3951.9414
150.0218-0.0178-0.00650.1087-0.01810.1125-0.1065-0.0099-0.1144-0.12160.02490.11410.09340.0811-0.0561.2479-0.1743-0.05740.58360.2970.34521.1602100.030842.1991
160.0038-0.00520.00180.0056-0.00280.00160.0273-0.0118-0.037-0.0398-0.06540.002-0.00450.092800.99750.24430.06291.0748-0.13960.8833-12.5781113.80652.2712
170.00050.0006-0.0006-0.0002-0.00190.00250.01720.00980.08130.00210.0134-0.0243-0.05520.0137-00.66550.2870.36231.23440.14730.7569-16.1391122.863360.6855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 34 through 114 )
2X-RAY DIFFRACTION2chain 'G' and (resid 115 through 190 )
3X-RAY DIFFRACTION3chain 'G' and (resid 191 through 235 )
4X-RAY DIFFRACTION4chain 'G' and (resid 236 through 353 )
5X-RAY DIFFRACTION5chain 'G' and (resid 354 through 474 )
6X-RAY DIFFRACTION6chain 'G' and (resid 475 through 505 )
7X-RAY DIFFRACTION7chain 'B' and (resid 521 through 526 )
8X-RAY DIFFRACTION8chain 'B' and (resid 527 through 534 )
9X-RAY DIFFRACTION9chain 'B' and (resid 535 through 544 )
10X-RAY DIFFRACTION10chain 'B' and (resid 545 through 572 )
11X-RAY DIFFRACTION11chain 'B' and (resid 573 through 595 )
12X-RAY DIFFRACTION12chain 'B' and (resid 596 through 605 )
13X-RAY DIFFRACTION13chain 'B' and (resid 606 through 615 )
14X-RAY DIFFRACTION14chain 'B' and (resid 616 through 625 )
15X-RAY DIFFRACTION15chain 'B' and (resid 626 through 647 )
16X-RAY DIFFRACTION16chain 'B' and (resid 648 through 657 )
17X-RAY DIFFRACTION17chain 'B' and (resid 658 through 664 )

+
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