[English] 日本語
Yorodumi
- EMDB-9109: Structural basis of coreceptor recognition by HIV-1 envelope spike -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9109
TitleStructural basis of coreceptor recognition by HIV-1 envelope spike
Map dataHIV-1 envelope spike
Sample
  • Complex: C-C chemokine receptor type 5 (CCR5) in complex with T-cell surface glycoprotein CD4 and HIV1 envelope glycoprotein gp120
    • Complex: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: T-cell surface glycoprotein CD4
      • Protein or peptide: T-cell surface glycoprotein CD4
    • Complex: C-C chemokine receptor type 5
      • Protein or peptide: C-C chemokine receptor type 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
KeywordsHIV coreceptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / chemokine receptor activity / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / signaling / T cell selection / MHC class II protein binding ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / chemokine receptor activity / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / signaling / T cell selection / MHC class II protein binding / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / C-C chemokine binding / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / response to cholesterol / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Other interleukin signaling / dendritic cell chemotaxis / extracellular matrix structural constituent / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Interleukin-10 signaling / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / macrophage differentiation / regulation of calcium ion transport / Generation of second messenger molecules / T cell differentiation / Co-inhibition by PD-1 / positive regulation of protein kinase activity / Binding and entry of HIV virion / cellular defense response / coreceptor activity / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / host cell endosome membrane / cell chemotaxis / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / positive regulation of T cell activation / chemotaxis / calcium ion transport / MHC class II protein complex binding / transmembrane signaling receptor activity / MAPK cascade / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / signaling receptor activity / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / actin binding / virus receptor activity / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / defense response to Gram-negative bacterium / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / endosome / cell adhesion / immune response / G protein-coupled receptor signaling pathway / inflammatory response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host endosome membrane / apoptotic process / lipid binding / viral envelope / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / enzyme binding / cell surface / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding
Similarity search - Function
CC chemokine receptor 5 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Chemokine receptor family / : ...CC chemokine receptor 5 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Chemokine receptor family / : / Immunoglobulin / Immunoglobulin domain / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / C-C chemokine receptor type 5 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsShaik MM / Chen B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI141002 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of coreceptor recognition by HIV-1 envelope spike.
Authors: Md Munan Shaik / Hanqin Peng / Jianming Lu / Sophia Rits-Volloch / Chen Xu / Maofu Liao / Bing Chen /
Abstract: HIV-1 envelope glycoprotein (Env), which consists of trimeric (gp160) cleaved to (gp120 and gp41), interacts with the primary receptor CD4 and a coreceptor (such as chemokine receptor CCR5) to fuse ...HIV-1 envelope glycoprotein (Env), which consists of trimeric (gp160) cleaved to (gp120 and gp41), interacts with the primary receptor CD4 and a coreceptor (such as chemokine receptor CCR5) to fuse viral and target-cell membranes. The gp120-coreceptor interaction has previously been proposed as the most crucial trigger for unleashing the fusogenic potential of gp41. Here we report a cryo-electron microscopy structure of a full-length gp120 in complex with soluble CD4 and unmodified human CCR5, at 3.9 Å resolution. The V3 loop of gp120 inserts into the chemokine-binding pocket formed by seven transmembrane helices of CCR5, and the N terminus of CCR5 contacts the CD4-induced bridging sheet of gp120. CCR5 induces no obvious allosteric changes in gp120 that can propagate to gp41; it does bring the Env trimer close to the target membrane. The N terminus of gp120, which is gripped by gp41 in the pre-fusion or CD4-bound Env, flips back in the CCR5-bound conformation and may irreversibly destabilize gp41 to initiate fusion. The coreceptor probably functions by stabilizing and anchoring the CD4-induced conformation of Env near the cell membrane. These results advance our understanding of HIV-1 entry into host cells and may guide the development of vaccines and therapeutic agents.
History
DepositionSep 7, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseDec 12, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6met
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9109.png

Downloads & links

-
Map

FileDownload / File: emd_9109.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 envelope spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 317.7 Å		1.06 Å/pix.
x 300 pix.
= 317.7 Å		1.06 Å/pix.
x 300 pix.
= 317.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.057979748 - 0.12776032
Average (Standard dev.)0.00030304125 (±0.0038826352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z317.700317.700317.700
α/β/γ90.00090.00090.000
start NX/NY/NZ-153-266-98
NX/NY/NZ528514389
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0580.1280.000

-
Supplemental data

-
Mask #1

Fileemd_9109_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: HIV-1 envelope spike

Fileemd_9109_half_map_1.map
AnnotationHIV-1 envelope spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: HIV-1 envelope spike

Fileemd_9109_half_map_2.map
AnnotationHIV-1 envelope spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C-C chemokine receptor type 5 (CCR5) in complex with T-cell surfa...

EntireName: C-C chemokine receptor type 5 (CCR5) in complex with T-cell surface glycoprotein CD4 and HIV1 envelope glycoprotein gp120
Components
  • Complex: C-C chemokine receptor type 5 (CCR5) in complex with T-cell surface glycoprotein CD4 and HIV1 envelope glycoprotein gp120
    • Complex: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: T-cell surface glycoprotein CD4
      • Protein or peptide: T-cell surface glycoprotein CD4
    • Complex: C-C chemokine receptor type 5
      • Protein or peptide: C-C chemokine receptor type 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose

-
Supramolecule #1: C-C chemokine receptor type 5 (CCR5) in complex with T-cell surfa...

SupramoleculeName: C-C chemokine receptor type 5 (CCR5) in complex with T-cell surface glycoprotein CD4 and HIV1 envelope glycoprotein gp120
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 200 MDa

-
Supramolecule #2: Envelope glycoprotein gp160

SupramoleculeName: Envelope glycoprotein gp160 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1

-
Supramolecule #3: T-cell surface glycoprotein CD4

SupramoleculeName: T-cell surface glycoprotein CD4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: C-C chemokine receptor type 5

SupramoleculeName: C-C chemokine receptor type 5 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.465043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DNLWVTVYYG VPVWKEATTT LFCASDAKAY KAEVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNNMV EQMHEDIISL WDQSLKPCV KLTPLCVTLN CIDLNNSTNN NNSSGVKTGI DKGEIKNCSF NTTTSVKDKE KKEYALFYNL DVVQIGNDNT S YRLTSCNT ...String:
DNLWVTVYYG VPVWKEATTT LFCASDAKAY KAEVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNNMV EQMHEDIISL WDQSLKPCV KLTPLCVTLN CIDLNNSTNN NNSSGVKTGI DKGEIKNCSF NTTTSVKDKE KKEYALFYNL DVVQIGNDNT S YRLTSCNT SVITQACPKV TFEPIPIHYC TPAGYAILKC NGKKFNGTGP CTNVSTVQCT HGIKPVVSTQ LLLNGSLAEE DI VIRSENL TNNAKTIIVQ LKDPVDINCT RPNNNTRKSI HIGPGRAFYA TGDIIGDIRQ AHCNLSRAQW NDTLSKIVTK LRE QFENKT IKFQPPSGGD PEIVFHSFNC GGEFFYCNTT QLFNSTWTNN TEGTSNTTGN DTITLPCRIK QIVNMWQEVG KAMY APPIK GKIKCSSNIT GLLLTRDGGN NEMNTTEIFR PGGGDMRDNW RSELYKYKVV RIEPLG

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #2: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.455477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KKVVLGKKGD TVELTCTASQ KKSIQFHWKN SNQIKILGNQ GSFLTKGPSK LNDRADSRRS LWDQGNFPLI IKNLKIEDSD TYICEVEDQ KEEVQLLVFG LTANSDTHLL QGQSLTLTLE SPPGSSPSVQ CRSPRGKNIQ GGKTLSVSQL ELQDSGTWTC T VLQNQKKV ...String:
KKVVLGKKGD TVELTCTASQ KKSIQFHWKN SNQIKILGNQ GSFLTKGPSK LNDRADSRRS LWDQGNFPLI IKNLKIEDSD TYICEVEDQ KEEVQLLVFG LTANSDTHLL QGQSLTLTLE SPPGSSPSVQ CRSPRGKNIQ GGKTLSVSQL ELQDSGTWTC T VLQNQKKV EFKIDIVVLA FQKASSIVYK KEGEQVEFSF PLAFTVEKLT GSGELWWQAE RASSSKSWIT FDLKNKEVSV KR VTQDPKL QMGKKLPLHL TLPQALPQYA GSGNLTLALE AKTGKLHQEV NLVVMRATQL QKNLTCEVWG PTSPKLMLSL KLE NKEAKV SKREKAVWVL NPEAGMWQCL LSDSGQVLLE SNIKVLP

UniProtKB: T-cell surface glycoprotein CD4

-
Macromolecule #3: C-C chemokine receptor type 5

MacromoleculeName: C-C chemokine receptor type 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.343008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYQVSSPI(TYS) DIN(TYS)YTSEPC QKINVKQIAA RLLPPLYSLV FIFGFVGNML VILILINCKR LKSMTDIYLL NL AISDLFF LLTVPFWAHY AAAQWDFGNT MCQLLTGLYF IGFFSGIFFI ILLTIDRYLA VVHAVFALKA RTVTFGVVTS VIT WVVAVF ...String:
MDYQVSSPI(TYS) DIN(TYS)YTSEPC QKINVKQIAA RLLPPLYSLV FIFGFVGNML VILILINCKR LKSMTDIYLL NL AISDLFF LLTVPFWAHY AAAQWDFGNT MCQLLTGLYF IGFFSGIFFI ILLTIDRYLA VVHAVFALKA RTVTFGVVTS VIT WVVAVF ASLPGIIFTR SQKEGLHYTC SSHFPYSQYQ FWKNFQTLKI VILGLVLPLL VMVICYSGIL KTLLRCRNEK KRHR AVRLI FTIMIVYFLF WAPYNIVLLL NTFQEFFGLN NCSSSNRLDQ AMQVTETLGM THCCINPIIY AFVGEKFRNY LLVFF Q

UniProtKB: C-C chemokine receptor type 5

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #8: 2-acetamido-2-deoxy-alpha-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-galactopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: A2G
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationName
100.0 mMTris
150.0 mMSodium Chloride
1.0 mMEDTA
0.025 %DDM
0.001 %LMNG
0.04 %Cholesterol Hemisuccinate

Details: 100 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.001% LMNG (w/v), 0.025% DDM (w/v), and 0.04 % CHS (w/v).
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 307346
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 307346
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 16
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5uiw

chain_id: A, source_name: PDB, initial_model_type: experimental model

1wio

chain_id: A, source_name: PDB, initial_model_type: experimental model

2qad

chain_id: G, source_name: PDB, initial_model_type: experimental model

5vn3

chain_id: G, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 200
Output model

PDB-6met:
Structural basis of coreceptor recognition by HIV-1 envelope spike

+
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