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- EMDB-8713: Cryo-EM reconstruction of B41 SOSIP.664 in complex with soluble C... -

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Basic information

Entry
Database: EMDB / ID: EMD-8713
TitleCryo-EM reconstruction of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding of 17b
Map dataB41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
Sample
  • Complex: HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding
    • Complex: HIV-1 Env B41 SOSIP.664
      • Protein or peptide: 17b Fab light chain
      • Protein or peptide: 17b Fab heavy chain
    • Complex: CD4 (2-domain)
      • Protein or peptide: T-cell surface glycoprotein CD4
    • Complex: 17b fragment antigen
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...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 / 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 / positive regulation of kinase activity / 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 / 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 calcium-mediated signaling / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / protein tyrosine kinase binding / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / virus-mediated perturbation of host defense response / T cell activation / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / virus receptor activity / signaling receptor activity / Clathrin-mediated endocytosis / MHC class II protein complex binding / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / viral protein processing / early endosome / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / 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 / 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: 3.7 Å
AuthorsPallesen J / Ozorowski G / de Val N / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: Nature / Year: 2017
Title: Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike.
Authors: Gabriel Ozorowski / Jesper Pallesen / Natalia de Val / Dmitry Lyumkis / Christopher A Cottrell / Jonathan L Torres / Jeffrey Copps / Robyn L Stanfield / Albert Cupo / Pavel Pugach / John P ...Authors: Gabriel Ozorowski / Jesper Pallesen / Natalia de Val / Dmitry Lyumkis / Christopher A Cottrell / Jonathan L Torres / Jeffrey Copps / Robyn L Stanfield / Albert Cupo / Pavel Pugach / John P Moore / Ian A Wilson / Andrew B Ward /
Abstract: For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for ...For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for replication. The envelope glycoprotein (Env) trimer on the surface of HIV is responsible for receptor binding and fusion. Although Env can tolerate a high degree of mutation in five variable regions (V1-V5), and also at N-linked glycosylation sites that contribute roughly half the mass of Env, the functional sites for recognition of receptor CD4 and co-receptor CXCR4/CCR5 are conserved and essential for viral fitness. Soluble SOSIP Env trimers are structural and antigenic mimics of the pre-fusion native, surface-presented Env, and are targets of broadly neutralizing antibodies. Thus, they are attractive immunogens for vaccine development. Here we present high-resolution cryo-electron microscopy structures of subtype B B41 SOSIP Env trimers in complex with CD4 and antibody 17b, or with antibody b12, at resolutions of 3.7 Å and 3.6 Å, respectively. We compare these to cryo-electron microscopy reconstructions of B41 SOSIP Env trimers with no ligand or in complex with either CD4 or the CD4-binding-site antibody PGV04 at 5.6 Å, 5.2 Å and 7.4 Å resolution, respectively. Consequently, we present the most complete description yet, to our knowledge, of the CD4-17b-induced intermediate and provide the molecular basis of the receptor-binding-induced conformational change required for HIV-1 entry into host cells. Both CD4 and b12 induce large, previously uncharacterized conformational rearrangements in the gp41 subunits, and the fusion peptide becomes buried in a newly formed pocket. These structures provide key details on the biological function of the type I viral fusion machine from HIV-1 as well as new templates for inhibitor design.
History
DepositionApr 28, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseJul 12, 2017-
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: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vn3
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8713.png

Downloads & links

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Map

FileDownload / File: emd_8713.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.17061247 - 0.3141209
Average (Standard dev.)0.00008046172 (±0.010144891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ00-41
NX/NY/NZ737384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1710.3140.000

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Supplemental data

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Additional map: B41 SOSIP.664 in complex with soluble CD4 (D1-D2)...

Fileemd_8713_additional.map
AnnotationB41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b, additional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B41 SOSIP.664 in complex with soluble CD4 (D1-D2)...

Fileemd_8713_half_map_1.map
AnnotationB41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B41 SOSIP.664 in complex with soluble CD4 (D1-D2)...

Fileemd_8713_half_map_2.map
AnnotationB41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b, half-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 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) an...

EntireName: HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding
Components
  • Complex: HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding
    • Complex: HIV-1 Env B41 SOSIP.664
      • Protein or peptide: 17b Fab light chain
      • Protein or peptide: 17b Fab heavy chain
    • Complex: CD4 (2-domain)
      • Protein or peptide: T-cell surface glycoprotein CD4
    • Complex: 17b fragment antigen
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) an...

SupramoleculeName: HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 630 KDa

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Supramolecule #2: HIV-1 Env B41 SOSIP.664

SupramoleculeName: HIV-1 Env B41 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #5
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #3: CD4 (2-domain)

SupramoleculeName: CD4 (2-domain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #4: 17b fragment antigen

SupramoleculeName: 17b fragment antigen / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #1: 17b Fab light chain

MacromoleculeName: 17b Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.425869 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELELTQSPAT LSVSPGERAT LSCRASESVS SDLAWYQQKP GQAPRLLIYG ASTRATGVPA RFSGSGSGAE FTLTISSLQS EDFAVYYCQ QYNNWPPRYT FGQGTRLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
ELELTQSPAT LSVSPGERAT LSCRASESVS SDLAWYQQKP GQAPRLLIYG ASTRATGVPA RFSGSGSGAE FTLTISSLQS EDFAVYYCQ QYNNWPPRYT FGQGTRLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRG

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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: 17.357824 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAFILG FLGAAGSTMG AASMALTVQA RLLLSGIVQQ QNNLLRAPEA QQHMLQLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KIICCTNVPW NDSWSNKTIN EIWDNMTWMQ WEKEIDNYTQ HIYTLLEVSQ IQQEKNEQEL LELD

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Macromolecule #3: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.702469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCNNV NTNNTNNSTN ATISDWEKME T GEMKNCSF ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCNNV NTNNTNNSTN ATISDWEKME T GEMKNCSF NVTTSIRDKI KKEYALFYKL DVVPLENKNN INNTNITNYR LINCNTSVIT QACPKVSFEP IPIHYCAPAG FA ILKCNSK TFNGSGPCTN VSTVQCTHGI RPVVSTQLLL NGSLAEEEIV IRSENITDNA KTIIVQLNEA VEINCTRPNN NTR KSIHIG PGRAFYATGD IIGNIRQAHC NISKARWNET LGQIVAKLEE QFPNKTIIFN HSSGGDPEIV THSFNCGGEF FYCN TTPLF NSTWNNTRTD DYPTGGEQNI TLQCRIKQII NMWQGVGKAM YAPPIRGQIR CSSNITGLLL TRDGGRDQNG TETFR PGGG NMRDNWRSEL YKYKVVKIEP LGIAPTACKR RV

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Macromolecule #4: T-cell surface glycoprotein CD4

MacromoleculeName: T-cell surface glycoprotein CD4 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.50326 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 EFKIDIVVLA FQKASNT

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Macromolecule #5: 17b Fab heavy chain

MacromoleculeName: 17b Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.484455 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLESGAE VKKPGSSVKV SCKASGDTFI RYSFTWVRQA PGQGLEWMGR IITILDVAHY APHLQGRVTI TADKSTSTVY LELRNLRSD DTAVYFCAGV YEGEADEGEY DNNGFLKHWG QGTLVTVTSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLLESGAE VKKPGSSVKV SCKASGDTFI RYSFTWVRQA PGQGLEWMGR IITILDVAHY APHLQGRVTI TADKSTSTVY LELRNLRSD DTAVYFCAGV YEGEADEGEY DNNGFLKHWG QGTLVTVTSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP K

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
50.0 mMTris
0.06 mMDDM

Details: DDM was added to a final concentration of 0.06 mM prior to vitrification
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER
Details: 3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging.
DetailsB41 SOSIP.664 was incubated with a 6X molar excess of soluble CD4 and 17b Fab overnight at room temperature, purified by size exclusion chromatography, and concentrated prior to grid application

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 38168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 0.000131 µm / Digitization - Frames/image: 1-50 / Number real images: 1169 / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 7.5 degrees
Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.94 degrees
Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 46855
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsHomology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. sCD4 and 17b coordinates taken from PDB 1GC1. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: EMRinger
Output model

PDB-5vn3:
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b

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