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- EMDB-46653: Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-46653
TitleCryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated
Map dataHIV-1 BG505 SOSIP Env with sCD4 and VRC34.01 Fabs
Sample
  • Complex: HIV-1 BG505 SOSIP.664 Env in complex with 3 molecules of sCD4 and 3 VRc34.01 Fab fragments
    • Complex: HIV-1 BG505 SOSIP.664
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: 4-domain CD4
      • Protein or peptide: T-cell surface glycoprotein CD4
    • Complex: VRC34.01 Fab
      • Protein or peptide: VRC34.01 Fab Heavy Chain
      • Protein or peptide: VRC34.01 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsRecombinant protein / HIV-1 Env / CD4 / fusion peptide binning antibody VRC34.01 / Vaccine / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / 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 / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / Other interleukin signaling / extracellular matrix structural constituent / T cell receptor complex / enzyme-linked receptor protein signaling pathway / 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 / coreceptor activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / positive regulation of T cell activation / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / virus receptor activity / 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 / cell adhesion / viral protein processing / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / 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 / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / 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
T-cell surface glycoprotein CD4 / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsThakur B / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170752 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated
Authors: Thakur B / Acharya P
History
DepositionAug 20, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46653.png

Downloads & links

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Map

FileDownload / File: emd_46653.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 BG505 SOSIP Env with sCD4 and VRC34.01 Fabs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.16
Minimum - Maximum-38.274208000000002 - 55.686194999999998
Average (Standard dev.)-0.000000000000893 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46653_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46653_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 BG505 SOSIP.664 Env in complex with 3 molecules of sCD4 and...

EntireName: HIV-1 BG505 SOSIP.664 Env in complex with 3 molecules of sCD4 and 3 VRc34.01 Fab fragments
Components
  • Complex: HIV-1 BG505 SOSIP.664 Env in complex with 3 molecules of sCD4 and 3 VRc34.01 Fab fragments
    • Complex: HIV-1 BG505 SOSIP.664
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: 4-domain CD4
      • Protein or peptide: T-cell surface glycoprotein CD4
    • Complex: VRC34.01 Fab
      • Protein or peptide: VRC34.01 Fab Heavy Chain
      • Protein or peptide: VRC34.01 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 BG505 SOSIP.664 Env in complex with 3 molecules of sCD4 and...

SupramoleculeName: HIV-1 BG505 SOSIP.664 Env in complex with 3 molecules of sCD4 and 3 VRc34.01 Fab fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#5
Details: here one of the gp120 protomer is rotated outward while other gp120 promoters maintain prefusion orientation
Molecular weightTheoretical: 308 KDa

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Supramolecule #2: HIV-1 BG505 SOSIP.664

SupramoleculeName: HIV-1 BG505 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: 4-domain CD4

SupramoleculeName: 4-domain CD4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: VRC34.01 Fab

SupramoleculeName: VRC34.01 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Details: BG505 SOSIP.664 construct / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.508406 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String:
NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MI RSENITN NAKNILVQFN TPVQINCTRP NNNTRKSIRI GPGQAFYATG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHF GNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Details: BG505 SOSIP.664 construct / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: VRC34.01 Fab Heavy Chain

MacromoleculeName: VRC34.01 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.797615 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: QEVLVQSGAE VKKPGASVKV SCRAFGYTFT GNALHWVRQA PGQGLEWLGW INPHSGDTTT SQKFQGRVYM TRDKSINTAF LDVTRLTSD DTGIYYCARD KYYGNEAVGM DVWGQGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QEVLVQSGAE VKKPGASVKV SCRAFGYTFT GNALHWVRQA PGQGLEWLGW INPHSGDTTT SQKFQGRVYM TRDKSINTAF LDVTRLTSD DTGIYYCARD KYYGNEAVGM DVWGQGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPK

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Macromolecule #4: VRC34.01 Fab Light Chain

MacromoleculeName: VRC34.01 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.138766 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: DIQLTQSPSF LSASVGDKVT ITCRASQGVR NELAWYQQKP GKAPNLLIYY ASTLQSGVPS RFSATGSGTH FTLTVSSLQP EDFATYFCQ HMSSYPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQLTQSPSF LSASVGDKVT ITCRASQGVR NELAWYQQKP GKAPNLLIYY ASTLQSGVPS RFSATGSGTH FTLTVSSLQP EDFATYFCQ HMSSYPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG

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Macromolecule #5: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.952468 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString:
KKVVLGKKGD TVELTCTASQ KKSIQFHWKN SNQIKILGNQ GSFLTKGPSK LNDRADSRRS LWDQGNFPLI IKNLKIEDSD TYICEVEDQ KEEVQLL

UniProtKB: T-cell surface glycoprotein CD4

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / 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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.1 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1003651
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 274345
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9d8y:
Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated

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