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- PDB-5a8h: cryo-ET subtomogram averaging of BG505 SOSIP.664 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5a8h
Titlecryo-ET subtomogram averaging of BG505 SOSIP.664 in complex with sCD4, 17b, and 8ANC195
Components
  • (FAB OF BROADLY NEUTRALIZING ANTIBODY ...) x 4
  • HIV-1 GP120
  • T-CELL SURFACE GLYCOPROTEIN CD4
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / 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 / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / 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 / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / positive regulation of kinase activity / Nef Mediated CD4 Down-regulation / Alpha-defensins / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Dectin-2 family / 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 / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of plasma membrane raft polarization / 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 / 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 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 / apoptotic process / protein kinase binding / host cell plasma membrane / positive regulation of DNA-templated transcription / structural molecule activity / virion membrane / 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
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 23 Å
AuthorsScharf, L. / Wang, H. / Gao, H. / Chen, S. / McDowall, A. / Bjorkman, P.
CitationJournal: Cell / Year: 2015
Title: Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env.
Authors: Louise Scharf / Haoqing Wang / Han Gao / Songye Chen / Alasdair W McDowall / Pamela J Bjorkman /
Abstract: The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal ...The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal and electron microscopy (EM) structures of bNAb 8ANC195 complexed with monomeric gp120 and trimeric Env, respectively, spans the gp120 and gp41 Env subunits. To investigate 8ANC195's gp41 epitope at higher resolution, we solved a 3.58 Å crystal structure of 8ANC195 complexed with fully glycosylated Env trimer, revealing 8ANC195 insertion into a glycan shield gap to contact gp120 and gp41 glycans and protein residues. To determine whether 8ANC195 recognizes the CD4-bound open Env conformation that leads to co-receptor binding and fusion, one of several known conformations of virion-associated Env, we solved EM structures of an Env/CD4/CD4-induced antibody/8ANC195 complex. 8ANC195 binding partially closed the CD4-bound trimer, confirming structural plasticity of Env by revealing a previously unseen conformation. 8ANC195's ability to bind different Env conformations suggests advantages for potential therapeutic applications.
History
DepositionJul 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-3096
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 GP120
B: T-CELL SURFACE GLYCOPROTEIN CD4
C: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
D: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
E: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5
F: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5
G: HIV-1 GP120
H: T-CELL SURFACE GLYCOPROTEIN CD4
I: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
J: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
K: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5
L: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5
M: HIV-1 GP120
N: T-CELL SURFACE GLYCOPROTEIN CD4
O: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
P: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
Q: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5
R: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,13463
Polymers458,17918
Non-polymers9,95445
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 6 molecules AGMBHN

#1: Protein HIV-1 GP120


Mass: 34838.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Plasmid: PTT5 / Cell line (production host): HEK-6E / Production host: HOMO SAPIENS (human) / References: UniProt: P35961*PLUS
#2: Protein T-CELL SURFACE GLYCOPROTEIN CD4 / T-CELL SURFACE ANTIGEN T4/LEU-3 / CD4


Mass: 20503.260 Da / Num. of mol.: 3 / Fragment: SOLUBLE CD4 D1-D2 DOMAINS, RESIDUES26-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTT5 / Cell line (production host): HEK-6E / Production host: HOMO SAPIENS (human) / References: UniProt: P01730

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Antibody , 4 types, 12 molecules CIODJPEKQFLR

#3: Antibody FAB OF BROADLY NEUTRALIZING ANTIBODY 17B


Mass: 23399.898 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTT5 / Cell line (production host): HEK-6E / Production host: HOMO SAPIENS (human)
#4: Antibody FAB OF BROADLY NEUTRALIZING ANTIBODY 17B


Mass: 24457.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTT5 / Cell line (production host): HEK-6E / Production host: HOMO SAPIENS (human)
#5: Antibody FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5


Mass: 23401.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTT5 / Cell line (production host): HEK-6E / Production host: HOMO SAPIENS (human)
#6: Antibody FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G52K5


Mass: 26125.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTT5 / Cell line (production host): HEK-6E / Production host: HOMO SAPIENS (human)

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Sugars , 1 types, 45 molecules

#7: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: SOLUBLE HIV-1 ENV TRIMER BG505 SOSIP.664 IN COMPLEX WITH SOLUBLE CD4S (D1-D2), BROADLY NEUTRALIZING ANTIBODY 17B FABS, AND BROADLY NEUTRALIZING ANTIBODY 8ANC195 VARIANT G32K5 FABS
Type: COMPLEX
Buffer solutionName: 20MM TRIS, 50MM NACL / pH: 8 / Details: 20MM TRIS, 50MM NACL
SpecimenConc.: 0.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 95, TEMPERATURE- 70, INSTRUMENT- FEI

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jan 25, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 41000 X / Cs: 2.2 mm
Specimen holderTilt angle max: 60 ° / Tilt angle min: -60 °
Image recordingElectron dose: 120 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 25
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EMAN23D reconstruction
3IMOD3D reconstruction
4PEET3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SUBTOMOGRAM AVERAGING / Resolution: 23 Å / Num. of particles: 1745 / Actual pixel size: 2.6 Å
Details: SUBTOMOGRAM AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3096. (DEPOSITION ID: 13596).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 1RZK

1rzk

RefinementHighest resolution: 23 Å
Refinement stepCycle: LAST / Highest resolution: 23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31242 0 630 0 31872

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