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- PDB-5a7x: negative stain EM of BG505 SOSIP.664 in complex with sCD4, 17b, a... -

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Basic information

Entry
Database: PDB / ID: 5a7x
Titlenegative stain EM of BG505 SOSIP.664 in complex with sCD4, 17b, and 8ANC195
Components
  • (FAB OF BROADLY NEUTRALIZING ANTIBODY ...) x 4
  • HIV-1 YU2 GP120
  • T-CELL SURFACE GLYCOPROTEIN CD4
KeywordsVIRAL PROTEIN
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 / enzyme-linked receptor protein signaling pathway / Other interleukin signaling / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Dectin-2 family / 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 / virus-mediated perturbation of host defense response / T cell activation / host cell endosome membrane / positive regulation of interleukin-2 production / calcium-mediated signaling / Vpu mediated degradation of CD4 / 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 / adaptive immune response / positive regulation of MAPK cascade / 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 / membrane raft / positive regulation of protein phosphorylation / 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 / membrane / 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
T-cell surface glycoprotein CD4 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 17 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 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Data collection / Category: atom_site / database_PDB_caveat / em_software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 2.1Jul 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

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3086
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 YU2 GP120
B: T-CELL SURFACE GLYCOPROTEIN CD4
C: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
D: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
E: HIV-1 YU2 GP120
F: T-CELL SURFACE GLYCOPROTEIN CD4
G: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
H: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
I: HIV-1 YU2 GP120
J: T-CELL SURFACE GLYCOPROTEIN CD4
K: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
L: FAB OF BROADLY NEUTRALIZING ANTIBODY 17B
M: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195
N: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195
O: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195
P: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195
Q: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195
R: FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,01463
Polymers457,05918
Non-polymers9,95445
Water0
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 AEIBFJ

#1: Protein HIV-1 YU2 GP120


Mass: 34838.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: YU2 / Plasmid: PTT5 / Cell line (production host): HEK293-6E / Production host: HOMO SAPIENS (human) / References: UniProt: P35961*PLUS
#2: Protein T-CELL SURFACE GLYCOPROTEIN CD4 / T-CELL SURFACE ANTIGEN T4/LEU-3


Mass: 20129.896 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): HEK293-6E / Production host: HOMO SAPIENS (human) / References: UniProt: P01730

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Antibody , 4 types, 12 molecules CGKDHLMOQNPR

#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): HEK293-6E / 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): HEK293-6E / Production host: HOMO SAPIENS (human)
#5: Antibody FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195


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): HEK293-6E / Production host: HOMO SAPIENS (human)
#6: Antibody FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195


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): HEK293-6E / 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 / N-Acetylglucosamine


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: single particle reconstruction

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Sample preparation

ComponentName: BG505 SOSIP.664 IN COMPLEX WITH 17B, SCD4, AND 8ANC195
Type: COMPLEX
Buffer solutionName: 20MM TRIS, 50 MM NACL / pH: 8 / Details: 20MM TRIS, 50 MM NACL
SpecimenConc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate
Specimen supportDetails: HOLEY CARBON

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12 / Date: Apr 7, 2015
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Cs: 2.2 mm
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k)
Image scansNum. digital images: 642

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EMAN23D reconstruction
3RELION3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionMethod: REFERENCE-BASED REFINEMENT / Resolution: 17 Å / Num. of particles: 7174 / Actual pixel size: 2.5 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3086. (DEPOSITION ID: 13327).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--MANUAL DOCKING AND LOCAL CORRELATION
RefinementHighest resolution: 17 Å
Refinement stepCycle: LAST / Highest resolution: 17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31242 0 630 0 31872

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