[English] 日本語
Yorodumi
- PDB-6cuf: Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibod... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6cuf
TitleCryo-EM structure at 4.2 A resolution of vaccine-elicited antibody vFP1.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
Components
  • (Envelope glycoprotein ...) x 2
  • PGT122 Heavy chain
  • PGT122 light chain
  • VRC03 heavy chain
  • VRC03 light chain
  • vFP1.01 Light chain
  • vFP1.01 heavy chain
KeywordsVIRAL PROTEIN / HIV-1 Env / BG505 SOSIP / fusion peptide / VRC03 / PGT122 / vFP7.04
Function / homologyRetroviral envelope protein / Envelope glycoprotein Gp160 / Envelope glycoprotein GP120 / Retroviral envelope protein GP41-like / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Gp120 core superfamily / membrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / virion attachment to host cell ...Retroviral envelope protein / Envelope glycoprotein Gp160 / Envelope glycoprotein GP120 / Retroviral envelope protein GP41-like / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Gp120 core superfamily / membrane fusion involved in viral entry into host cell / host cell 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 sourceMus musculus (house mouse)
Homo sapiens (human)
Human immunodeficiency virus 1
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 25, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 25, 2018Structure modelrepositoryInitial release
1.1Oct 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-7622
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7622
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
3: vFP1.01 heavy chain
4: vFP1.01 Light chain
5: PGT122 Heavy chain
6: PGT122 light chain
7: VRC03 light chain
8: VRC03 heavy chain
C: Envelope glycoprotein gp120
D: Envelope glycoprotein gp41
H: vFP1.01 heavy chain
L: vFP1.01 Light chain
M: PGT122 Heavy chain
N: PGT122 light chain
Q: VRC03 heavy chain
R: VRC03 light chain
h: vFP1.01 heavy chain
l: vFP1.01 Light chain
m: PGT122 Heavy chain
n: PGT122 light chain
q: VRC03 heavy chain
r: VRC03 light chain
2: Envelope glycoprotein gp120
A: Envelope glycoprotein gp41
c: Envelope glycoprotein gp41
d: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,154186
Polyers508,15124
Non-polymers33,003162
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein/peptide , 6 types, 18 molecules 3Hh4Ll5Mm6Nn7Rr8Qq

#1: Protein/peptide vFP1.01 heavy chain


Mass: 22972.848 Da / Num. of mol.: 3 / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Protein/peptide vFP1.01 Light chain


Mass: 24127.859 Da / Num. of mol.: 3 / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide PGT122 Heavy chain


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


Mass: 11423.534 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Protein/peptide VRC03 light chain


Mass: 11386.774 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Protein/peptide VRC03 heavy chain


Mass: 14506.331 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Envelope glycoprotein ... , 2 types, 6 molecules C2dDAc

#7: Protein/peptide Envelope glycoprotein gp120 /


Mass: 52964.922 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#8: Protein/peptide Envelope glycoprotein gp41


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

-
Non-polymers , 3 types, 162 molecules

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


Mass: 221.208 Da / Num. of mol.: 93 / Formula: C8H15NO6 / N-Acetylglucosamine
#10: Chemical...
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 27 / Formula: C6H12O6
#11: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 42 / Formula: C6H12O6

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1vFP1.01-BG505 DS-SOSIP-VRC03-PGT122COMPLEX1,2,3,4,5,60MULTIPLE SOURCES
2PGT122COMPLEX3,41RECOMBINANT
3VRC03COMPLEX5,61RECOMBINANT
4vFP1.01COMPLEX1,21RECOMBINANT
5BG505 DS-SOSIPCOMPLEX7, 81RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
229606Homo sapiens (human)
339606Homo sapiens (human)
4410090Mus musculus (house mouse)
5511676Human immunodeficiency virus 1
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: 130000 / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70.28 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 864
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
9PHENIX1.13-2998-000model refinement
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 108758
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 44652 / Symmetry type: POINT
Atomic model buildingOverall b value: 142 / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Correlation Coefficient
Least-squares processHighest resolution: 4.2 Å

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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