[English] 日本語
Yorodumi
- PDB-3dno: Molecular structure for the HIV-1 gp120 trimer in the CD4-bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dno
TitleMolecular structure for the HIV-1 gp120 trimer in the CD4-bound state
Components(HIV-1 envelope glycoprotein gp120) x 3
KeywordsVIRAL PROTEIN / HIV-1 / ENVELOPE GLYCOPROTEIN / IMMUNODEFICIENCY VIRUS / gp120 / AIDS / Apoptosis / Cleavage on pair of basic residues / Envelope protein / Fusion protein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Viral immunoevasion / Virion
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / 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 speciesHIV-1 M:B_HXB2R (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsBorgnia, M.J. / Liu, J. / Bartesaghi, A. / Sapiro, G. / Subramaniam, S.
CitationJournal: Nature / Year: 2008
Title: Molecular architecture of native HIV-1 gp120 trimers.
Authors: Jun Liu / Alberto Bartesaghi / Mario J Borgnia / Guillermo Sapiro / Sriram Subramaniam /
Abstract: The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. ...The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms trimers on the surface of the viral membrane. Using cryo-electron tomography combined with three-dimensional image classification and averaging, we report the three-dimensional structures of trimeric Env displayed on native HIV-1 in the unliganded state, in complex with the broadly neutralizing antibody b12 and in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal structures of the monomeric gp120 core in the b12- and CD4/17b-bound conformations into the density maps derived by electron tomography, we derive molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound states. We demonstrate that CD4 binding results in a major reorganization of the Env trimer, causing an outward rotation and displacement of each gp120 monomer. This appears to be coupled with a rearrangement of the gp41 region along the central axis of the trimer, leading to closer contact between the viral and target cell membranes. Our findings elucidate the structure and conformational changes of trimeric HIV-1 gp120 relevant to antibody neutralization and attachment to target cells.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_ref_seq_dif.details

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5020
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 envelope glycoprotein gp120
B: HIV-1 envelope glycoprotein gp120
C: HIV-1 envelope glycoprotein gp120
D: HIV-1 envelope glycoprotein gp120
E: HIV-1 envelope glycoprotein gp120
F: HIV-1 envelope glycoprotein gp120
G: HIV-1 envelope glycoprotein gp120
H: HIV-1 envelope glycoprotein gp120
I: HIV-1 envelope glycoprotein gp120


Theoretical massNumber of molelcules
Total (without water)96,3809
Polymers96,3809
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein/peptide HIV-1 envelope glycoprotein gp120 / SU / Glycoprotein 120 / gp120


Mass: 4225.840 Da / Num. of mol.: 3 / Fragment: Core: Residues 90-124
Source method: isolated from a genetically manipulated source
Details: Human immunodeficiency virus type 1 / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: isolate HXB2 group M subtype B, BaL / Gene: env / Production host: Homo sapiens (human) / References: UniProt: P04578
#2: Protein HIV-1 envelope glycoprotein gp120 / SU / Glycoprotein 120 / gp120


Mass: 18570.014 Da / Num. of mol.: 3 / Fragment: Core: Residues 198-396
Source method: isolated from a genetically manipulated source
Details: Human immunodeficiency virus type 1 / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: isolate HXB2 group M subtype B, BaL / Gene: env / Production host: Homo sapiens (human) / References: UniProt: P04578
#3: Protein HIV-1 envelope glycoprotein gp120 / SU / Glycoprotein 120 / gp120


Mass: 9330.696 Da / Num. of mol.: 3 / Fragment: Core: Residues 410-492
Source method: isolated from a genetically manipulated source
Details: Human immunodeficiency virus type 1 / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: isolate HXB2 group M subtype B, BaL / Gene: env / Production host: Homo sapiens (human) / References: UniProt: P04578
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeParent-ID
1HIV-1 BaLCOMPLEX0
2HIV-1 Envelope Glycoprotein GP1201
Details of virusHost category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens / Strain: SupT1-CCR5 CL.30
Buffer solutionName: 0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA / pH: 7.2 / Details: 0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Home made holey-carbon
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: Ethane 77K 100%RH Vitrobot

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 34000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.2 mm
Specimen holderTemperature: 90 K / Tilt angle max: 70 ° / Tilt angle min: -70 °
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GENERIC CCD

-
Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2IMOD3D reconstruction
CTF correctionDetails: No CTF correction applied
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionMethod: Tomographic reconstruction Weighted Back Projection / Resolution: 20 Å / Nominal pixel size: 0.41 Å
Details: IMOD was used for tomographic reconstruction. Programs developed in-house were used for alignment and classification of individual tomographic volumes. The final map is the average of ~4000 individual spikes.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Details: METHOD--Automatic. The coordinates for this entry and the two related entries 3DNL and 3DNN are based on fitting 1GC1 coordinates for the gp120 monomer deposited previously by Kwong et al in ...Details: METHOD--Automatic. The coordinates for this entry and the two related entries 3DNL and 3DNN are based on fitting 1GC1 coordinates for the gp120 monomer deposited previously by Kwong et al in 1998 into the density map for the trimer derived by electron microscopy. Therefore, authors did not deposit new structure factors, and, any features such as unusual torsion angles are the same as in the 1GC1 coordinates. REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1GC1

1gc1


Accession code: 1GC1 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 0 0 6738

+
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