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- EMDB-9108: Structural basis of coreceptor recognition by HIV-1 envelope spike -

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Basic information

Entry
Database: EMDB / ID: EMD-9108
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: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / phosphatidylinositol phospholipase C activity / C-C chemokine receptor activity / C-C chemokine binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / response to cholesterol / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Interleukin-10 signaling / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / cellular defense response / coreceptor activity / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / cell chemotaxis / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / calcium ion transport / chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / MAPK cascade / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / cell-cell signaling / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / actin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / early endosome / cell adhesion / endosome / inflammatory response / positive regulation of protein phosphorylation / immune response / membrane raft / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / external side of plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / structural molecule activity / virion membrane / positive regulation of DNA-templated transcription / enzyme binding / cell surface / signal transduction / protein homodimerization activity / zinc ion 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 / Chemokine receptor family / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin ...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 / Chemokine receptor family / Immunoglobulin C2-set / Immunoglobulin C2-set domain / 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: 3.9 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 6, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseDec 12, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6meo
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9108.png

Downloads & links

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Map

FileDownload / File: emd_9108.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: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.10970193 - 0.18590759
Average (Standard dev.)0.00033319413 (±0.005944809)
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-0.1100.1860.000

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Supplemental data

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Mask #1

Fileemd_9108_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 envelope spike

Fileemd_9108_half_map_1.map
AnnotationHIV-1 envelope spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 envelope spike

Fileemd_9108_half_map_2.map
AnnotationHIV-1 envelope spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose

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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

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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
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293T

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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)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293T

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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)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293T

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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

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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: 19.541176 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 EFKIDIVV

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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

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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

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Macromolecule #8: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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Macromolecule #9: 2-acetamido-2-deoxy-alpha-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-galactopyranose / type: ligand / ID: 9 / Number of copies: 1 / Formula: A2G
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Pressure: 0.0004 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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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

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.8)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 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)

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Atomic model buiding 1

Initial model
PDB IDChain

5uiw

chain_id: A

1wio

chain_id: A

2qad

chain_id: G

5vn3

chain_id: G
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 200
Output model

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

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