[English] 日本語
Yorodumi
- PDB-6cue: Cryo-EM structure at 4.0 A resolution of vaccine-elicited antibod... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6cue
TitleCryo-EM structure at 4.0 A resolution of vaccine-elicited antibody vFP7.04 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
Components
  • (Envelope glycoprotein ...) x 2
  • PGT122 Light chain
  • PGT122 heavy Chain
  • VRC03 Heavy chain
  • VRC03 light chain
  • vFP7.04 Heavy chain
  • vFP7.04 light chain
KeywordsVIRAL PROTEIN / HIV-1 Env / BG505 SOSIP / fusion peptide / VRC03 / PGT122 / vFP7.04
Function / homologyGp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization ...Gp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / host cell endosome membrane / evasion or tolerance by virus of host immune response / viral protein processing / fusion of virus membrane with host plasma membrane / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane / identical protein binding / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Function and homology information
Specimen sourceHuman immunodeficiency virus 1
Mus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsAcharya, P. / Carragher, B. / Potter, C.S. / Kwong, P.D.
CitationJournal: PLoS Pathog. / Year: 2018
Title: Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV.
Authors: Adam S Dingens / Priyamvada Acharya / Hugh K Haddox / Reda Rawi / Kai Xu / Gwo-Yu Chuang / Hui Wei / Baoshan Zhang / John R Mascola / Bridget Carragher / Clinton S Potter / Julie Overbaugh / Peter D Kwong / Jesse D Bloom
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 26, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Jul 18, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Oct 3, 2018Structure modelData collection / Refinement descriptionrefine_refine.pdbx_refine_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-7621
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7621
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
c: Envelope glycoprotein gp120
2: Envelope glycoprotein gp120
C: Envelope glycoprotein gp120
1: Envelope glycoprotein gp41
3: vFP7.04 Heavy chain
4: vFP7.04 light chain
5: PGT122 heavy Chain
6: PGT122 Light chain
7: VRC03 Heavy chain
8: VRC03 light chain
D: Envelope glycoprotein gp41
H: vFP7.04 Heavy chain
L: vFP7.04 light chain
M: PGT122 heavy Chain
N: PGT122 Light chain
Q: VRC03 Heavy chain
R: VRC03 light chain
d: Envelope glycoprotein gp41
h: vFP7.04 Heavy chain
l: vFP7.04 light chain
m: PGT122 heavy Chain
n: PGT122 Light chain
q: VRC03 Heavy chain
r: VRC03 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,910138
Polyers444,04724
Non-polymers23,863114
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Envelope glycoprotein ... , 2 types, 6 molecules c2C1Dd

#1: Protein/peptide Envelope glycoprotein gp120 / / Env polyprotein


Mass: 52986.969 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein/peptide Envelope glycoprotein gp41 / Env polyprotein


Mass: 17162.525 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S7

-
Protein/peptide , 6 types, 18 molecules 3Hh4Ll5Mm6Nn7Qq8Rr

#3: Protein/peptide vFP7.04 Heavy chain


Mass: 13152.787 Da / Num. of mol.: 3 / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Protein/peptide vFP7.04 light chain


Mass: 12256.805 Da / Num. of mol.: 3 / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Protein/peptide PGT122 heavy Chain


Mass: 14838.731 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Protein/peptide PGT122 Light chain


Mass: 11591.728 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: Protein/peptide VRC03 Heavy chain


Mass: 14639.500 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#8: Protein/peptide VRC03 light chain


Mass: 11386.774 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 114 molecules

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


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


Mass: 180.156 Da / Num. of mol.: 18 / Formula: C6H12O6
#11: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 15 / Formula: C6H12O6

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1vFP7.04-BG505 DS-SOSIP-VRC03-PGT122COMPLEX2,3,4,5,6,7,80MULTIPLE SOURCES
2PGT122COMPLEX5,61RECOMBINANT
3VRC03COMPLEX7,81RECOMBINANT
4GlycoproteinCOMPLEX3,41RECOMBINANT
5vFP7.04COMPLEX21RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
229606Homo sapiens (human)
339606Homo sapiens (human)
4411676Human immunodeficiency virus 1
5510090Mus musculus (house mouse)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
229606Homo sapiens (human)
339606Homo sapiens (human)
449606Homo sapiens (human)
559606Homo sapiens (human)
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE

-
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 / Calibrated magnification: 105000 / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53.11 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 978
Image scansMovie frames/image: 40 / Used frames/image: 1-40

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimera1.11.2model fitting
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.13-2998-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 152206
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 64580 / Symmetry type: POINT
Atomic model buildingOverall b value: 142 / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Correlation Coefficient
Least-squares processHighest resolution: 4 Å

+
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 EBI / 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