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- EMDB-39820: Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 mol... -

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Entry
Database: EMDB / ID: EMD-39820
TitleStructure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules
Map data
Sample
  • Complex: Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: T-cell surface glycoprotein CD4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / CRF_07BC / Env / CD4 / VIRUS
Function / homology
Function and homology information


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 / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of kinase activity / positive regulation of monocyte differentiation ...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 / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of kinase activity / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / 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 / coreceptor activity / positive regulation of plasma membrane raft polarization / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / host cell endosome membrane / T cell activation / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / MHC class II protein complex binding / Clathrin-mediated endocytosis / signaling receptor activity / virus receptor activity / clathrin-dependent endocytosis of virus by host cell / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / viral protein processing / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / endoplasmic reticulum membrane / virion attachment to host cell / protein kinase binding / apoptotic process / positive regulation of DNA-templated transcription / host cell plasma membrane / structural molecule activity / virion membrane / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
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 / Immunoglobulin / Immunoglobulin domain / Envelope glycoprotein Gp160 ...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 / 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 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein gp160 / T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLi D / Wang T
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Intermediate open state of CD4-bound HIV-1 env heterotrimers in asia CRFs.
Authors: Dan Li / Li Liu / Xuejun Ye / Yuyang Chen / Qiaoju Ren / ShaoJian Xu / Yan Ren / He Cao / Tao Wang /
Abstract: The HIV-1 envelope glycoprotein (Env) plays crucial role in viral infection by facilitating viral attachment to host cells and inducing fusion of the virus with the host cell membrane. This fusion ...The HIV-1 envelope glycoprotein (Env) plays crucial role in viral infection by facilitating viral attachment to host cells and inducing fusion of the virus with the host cell membrane. This fusion allows the HIV-1 viral genome to enter the target cell then triggering various stages of the viral life cycle. The native Env directly interacts with the main receptor CD4 and the co-receptor (CCR5 or CXCR4) in human cell membrane then induces membrane fusion. The elucidation of the structure of Env with CD4 and co-receptors in different HIV-1 subtypes is essential for the understanding of the mechanism of virus entry. Here we report the Cryo-EM structure of the CD4-bound HIV-1 heterotrimeric Env from Asia prevalent CRF07_BC CH119 strain. In this structure, the binding of three CD4 molecules with Env induced extensively conformational changes in gp120, resulting in the transformation of the Env from close state to intermediate open state. Additionally, the conformational shift of V1/V2 loops of the heterotrimeric Env allosterically expose the V3 loop and promoting the further interactions with co-receptor CCR5 or CXCR4. These findings not only illustrate the structural complexity and plasticity of HIV-1 Env but also give new insights how the biological trimeric Env initialize the immune recognition and membrane fusion.
History
DepositionApr 20, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39820.png

Downloads & links

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Map

FileDownload / File: emd_39820.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.049
Minimum - Maximum-1.1794897 - 1.5211313
Average (Standard dev.)0.00056501105 (±0.019692048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 415.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39820_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_39820_half_map_2.map
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Sample components

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Entire : Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 mol...

EntireName: Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules
Components
  • Complex: Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: T-cell surface glycoprotein CD4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 mol...

SupramoleculeName: Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 58.258125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAVGNL WVTVYYGVPV WKEATTTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQE LVLENVTENF NMWKNEMVNQ MHEDVISLWD QSLKPCVKLT PLCVTLECSK VSNNETDKYN GTEEMKNCSF N ATTVVRDR ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAVGNL WVTVYYGVPV WKEATTTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQE LVLENVTENF NMWKNEMVNQ MHEDVISLWD QSLKPCVKLT PLCVTLECSK VSNNETDKYN GTEEMKNCSF N ATTVVRDR QQKVYALFYR LDIVPLTEKN SSENSSKYYR LINCNTSAIT QACPKVSFEP IPIHYCTPAG YAILKCNDKT FN GTGPCHN VSTVQCTHGI KPVVSTQLLL NGSLAEGEII IRSENLTNNV KTILVHLNQS VEIVCTRPNN NTRKSIRIGP GQT FYATGD IIGDIRQAHC NISKWHETLK RVSEKLAEHF PNKTINFTSS SGGDLEITTH SFTCRGEFFY CNTSGLFNST YMPN GTYLH GDTNSNSSIT IPCRIKQIIN MWQEVGRAMY APPIEGNITC KSNITGLLLV RDGGTESNNT ETNNTEIFRP GGGDM RDNW RSELYKYKVV EIKPLGVAPT ACKRRVVERR RRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.285703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGVAGSTMG AASMTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHLLQLTVW GIKQLQTRVL AIERYLKDQQ LLGIWGCSG KLICCTAVPW NSSWSNKSQK EIWDNMTWMQ WDKEISNYTN TIYKLLEDSQ NQQESNEKDL LALDGGGGGH H HHHH

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.67532 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNRGVPFRHL LLVLQLALLP AATQGKKVVL GKKGDTVELT CTASQKKSIQ FHWKNSNQIK ILGNQGSFLT KGPSKLNDRA DSRRSLWDQ GNFPLIIKNL KIEDSDTYIC EVEDQKEEVQ LLVFGLTANS DTHLLQGQSL TLTLESPPGS SPSVQCRSPR G KNIQGGKT ...String:
MNRGVPFRHL LLVLQLALLP AATQGKKVVL GKKGDTVELT CTASQKKSIQ FHWKNSNQIK ILGNQGSFLT KGPSKLNDRA DSRRSLWDQ GNFPLIIKNL KIEDSDTYIC EVEDQKEEVQ LLVFGLTANS DTHLLQGQSL TLTLESPPGS SPSVQCRSPR G KNIQGGKT LSVSQLELQD SGTWTCTVLQ NQKKVEFKID IVVLAFQKAS SIVYKKEGEQ VEFSFPLAFT VEKLTGSGEL WW QAERASS SKSWITFDLK NKEVSVKRVT QDPKLQMGKK LPLHLTLPQA LPQYAGSGNL TLALEAKTGK LHQEVNLVVM RAT QLQKNL TCEVWGPTSP KLMLSLKLEN KEAKVSKREK AVWVLNPEAG MWQCLLSDSG QVLLESNIKV LPTWSTGSGH HHHH H

UniProtKB: T-cell surface glycoprotein CD4

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1045667
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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