[English] 日本語
Yorodumi
- PDB-6edu: B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-recepto... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6edu
TitleB41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195
Components
  • (8ANC195 G52K5 Fab ...) x 2
  • (Envelope glycoprotein ...) x 2
  • 21c Fab VH domain
  • 21c Fab VL domain
  • T-cell surface glycoprotein CD4
KeywordsIMMUNE SYSTEM / HIV-1 Env / broadly neutralizing antibodies / cryo-EM / single particle analysis / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyImmunoglobulin domain / Nef Mediated CD4 Down-regulation / Immunoglobulin C2-set domain / Vpu mediated degradation of CD4 / Immunoglobulin C2-set / Immunoglobulin subtype / Immunoglobulin subtype 2 / Binding and entry of HIV virion / Alpha-defensins / Phosphorylation of CD3 and TCR zeta chains ...Immunoglobulin domain / Nef Mediated CD4 Down-regulation / Immunoglobulin C2-set domain / Vpu mediated degradation of CD4 / Immunoglobulin C2-set / Immunoglobulin subtype / Immunoglobulin subtype 2 / Binding and entry of HIV virion / Alpha-defensins / Phosphorylation of CD3 and TCR zeta chains / Ig-like domain profile. / T-cell surface antigen CD4 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / CD4, extracellular / Envelope glycoprotein GP120 / Downstream TCR signaling / Immunoglobulin-like domain / Immunoglobulin V-set domain / PD-1 signaling / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / Clathrin-mediated endocytosis / T cell CD4 receptor C-terminal region / Cargo recognition for clathrin-mediated endocytosis / Other interleukin signaling / Retroviral envelope protein / Generation of second messenger molecules / Immunoglobulin-like fold / Immunoglobulin / Translocation of ZAP-70 to Immunological synapse / T cell CD4 receptor C terminal region / CD4, extracellular / helper T cell enhancement of adaptive immune response / interleukin-16 receptor activity / interleukin-16 binding / induction by virus of host cell-cell fusion / maintenance of protein location in cell / T cell selection / MHC class II protein binding / positive regulation of monocyte differentiation / positive regulation of kinase activity / regulation of T cell activation / response to vitamin D / T cell receptor complex / positive regulation of viral entry into host cell / interleukin-15-mediated signaling pathway / positive regulation of interleukin-2 biosynthetic process / enzyme linked receptor protein signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of calcium ion transport into cytosol / coreceptor activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / T cell differentiation / regulation of calcium ion transport / cytokine production / extracellular matrix structural constituent / immunoglobulin binding / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / positive regulation of protein kinase activity / protein tyrosine kinase binding / clathrin-coated vesicle membrane / actin filament reorganization / host cell endosome membrane / positive regulation of T cell proliferation / evasion or tolerance by virus of host immune response / entry into host cell / T cell activation / viral protein processing / regulation of defense response to virus by virus / virus receptor activity / transmembrane signaling receptor activity / membrane organization / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane receptor protein tyrosine kinase signaling pathway / adaptive immune response / fusion of virus membrane with host plasma membrane / positive regulation of MAPK cascade / T cell receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / response to estradiol / positive regulation of I-kappaB kinase/NF-kappaB signaling / signaling receptor activity / fusion of virus membrane with host endosome membrane / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / viral envelope / immune response / defense response to Gram-negative bacterium / cell adhesion / positive regulation of protein phosphorylation / virion attachment to host cell / membrane raft / external side of plasma membrane / endoplasmic reticulum lumen / host cell plasma membrane
Function and homology information
Specimen sourceHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.06 Å resolution
AuthorsBarnes, C.O. / Bjorkman, P.J.
Funding supportUnited States , 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesP50 GM082545-06United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesP01 AI100148United States
CitationJournal: Cell Host Microbe / Year: 2018
Title: Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion.
Authors: Haoqing Wang / Christopher O Barnes / Zhi Yang / Michel C Nussenzweig / Pamela J Bjorkman
Abstract: HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and ...HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and opening Env to enable gp41-mediated fusion. We present 3.54 Å and 4.06 Å cryoelectron microscopy structures of partially open soluble native-like Env trimers (SOSIPs) bound to CD4. One structure, a complex with a coreceptor-mimicking antibody that binds both CD4 and gp120, stabilizes the displaced V1V2 and reveals its structure. Comparing partially and fully open Envs with closed Envs shows that gp41 rearrangements are independent of the CD4-induced rearrangements that result in V1V2 displacement and formation of a 4-stranded bridging sheet. These findings suggest ordered conformational changes before coreceptor binding: (1) gp120 opening inducing side-chain rearrangements and a compact gp41 central helix conformation, and (2) 4-stranded bridging-sheet formation and V1V2 displacement. These analyses illuminate potential receptor-induced Env changes and inform design of therapeutics disrupting viral entry.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 11, 2018 / Release: Oct 17, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 17, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author / pdbx_database_related_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_database_related.content_type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
E: Envelope glycoprotein gp160
F: Envelope glycoprotein gp160
G: T-cell surface glycoprotein CD4
H: T-cell surface glycoprotein CD4
I: T-cell surface glycoprotein CD4
J: 21c Fab VH domain
K: 21c Fab VL domain
L: 21c Fab VH domain
M: 21c Fab VL domain
N: 21c Fab VH domain
O: 21c Fab VL domain
P: 8ANC195 G52K5 Fab VH domain
Q: 8ANC195 G52K5 Fab VL domain
R: 8ANC195 G52K5 Fab VH domain
S: 8ANC195 G52K5 Fab VL domain
T: 8ANC195 G52K5 Fab VH domain
U: 8ANC195 G52K5 Fab VL domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)603,061144
Polyers577,57721
Non-polymers25,484123
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)85940
ΔGint (kcal/M)189
Surface area (Å2)145590

-
Components

-
Envelope glycoprotein ... , 2 types, 6 molecules ABCDEF

#1: Protein/peptide Envelope glycoprotein gp160


Mass: 17357.824 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): K1 / References: UniProt: B3UEZ6
#2: Protein/peptide Envelope glycoprotein gp160


Mass: 57702.469 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): K1 / References: UniProt: B3UES2

-
Protein/peptide , 3 types, 9 molecules GHIJLNKMO

#3: Protein/peptide T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 20503.260 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01730
#4: Protein/peptide 21c Fab VH domain


Mass: 24619.590 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#5: Protein/peptide 21c Fab VL domain


Mass: 22815.264 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
8ANC195 G52K5 Fab ... , 2 types, 6 molecules PRTQSU

#6: Protein/peptide 8ANC195 G52K5 Fab VH domain


Mass: 26125.270 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#7: Protein/peptide 8ANC195 G52K5 Fab VL domain


Mass: 23401.984 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 123 molecules

#8: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 81 / Formula: C8H15NO6 / N-Acetylglucosamine
#9: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12 / Formula: C6H12O6
#10: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 30 / Formula: C6H12O6

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: B41 SOSIP-sCD4-21c-8ANC195 complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: RECOMBINANT
Molecular weightValue: 0.7 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTrisTris1
2125 mMSodium ChlorideNaCl1
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 0.26 mA / Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2531
Image scansMovie frames/image: 50

-
Processing

SoftwareName: PHENIX / Version: 1.14_3219: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4CTFFIND4.1CTF correctionPerformed CTF correction on movies
7UCSF Chimera1.11model fitting
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 305469 / Number of class averages: 4 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient
Least-squares processHighest resolution: 4.06 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010027005
ELECTRON MICROSCOPYf_angle_d1.327836936
ELECTRON MICROSCOPYf_chiral_restr0.06724515
ELECTRON MICROSCOPYf_plane_restr0.00874512
ELECTRON MICROSCOPYf_dihedral_angle_d7.773815726

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more