[English] 日本語
Yorodumi
- EMDB-7861: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7861
TitleFull length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab
Map dataFull length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, primary map
Sample
  • Complex: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64_13C Fab
    • Protein or peptide: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151, Light chain
    • Protein or peptide: Immunoglobulin G PCT64_13C Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PCT64_13C, Light chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsBerndsen ZT / Rantalainen K / Ward AB
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
History
DepositionMay 9, 2018-
Header (metadata) releaseMay 30, 2018-
Map releaseJun 27, 2018-
UpdateJun 27, 2018-
Current statusJun 27, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7861.png

Downloads & links

-
Map

FileDownload / File: emd_7861.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å		4.1 Å/pix.
x 100 pix.
= 410. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.043247964 - 0.17709337
Average (Standard dev.)0.00019345406 (±0.008554267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0430.1770.000

-
Supplemental data

-
Half map: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in...

Fileemd_7861_half_map_1.map
AnnotationFull length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in...

Fileemd_7861_half_map_2.map
AnnotationFull length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in compl...

EntireName: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64_13C Fab
Components
  • Complex: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64_13C Fab
    • Protein or peptide: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151, Light chain
    • Protein or peptide: Immunoglobulin G PCT64_13C Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PCT64_13C, Light chain

-
Supramolecule #1: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in compl...

SupramoleculeName: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64_13C Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

-
Macromolecule #1: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054

MacromoleculeName: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVRGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFNMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRKNVTG GNLTEDGKEE LKNCSFNATT ELRNKRQKVH ...String:
MKVRGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFNMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRKNVTG GNLTEDGKEE LKNCSFNATT ELRNKRQKVH SLFYRLDLVE LNEGNSSNSN TSMYRLINCN TSAITQACPK VSFEPIPIHY CAPAGFAILK CREEEFNGTG PCKNVSTVQC THGIKPVVST QLLLNGSLAE GTVKIRCENI SNNAKTILVQ LTTPVRINCT RPNNNTRTSI RIGPGQSFYA TGDIIGDIRK AYCNVSGSEW KEALGKVVVQ LRSHFNKTIT FASSSGGDLE ITTHSFNCGG EFFYCNTSSL FNSTWDGNST TNSTQEPNGT ITLPCRIKQI INMWQRTGQA MYAPPIPGKI RCDSNITGLI LTRDGENNNT ESETFRPEGG DMRNNWRSEL YKYKVVKIDP LGVAPTGAKR RVVEREKRAV GIGAVLFGFL GAAGSTMGAA SLTLTVQARQ LLSGIVQQQS NLLRAIEAQQ HLLRLTVWGI KQLQARVLAV ERYLSDQQLL GIWGCSGKLI CTTTVPWNSS WSNKSQDEIW NNMTWLQWDK EISNYTDTIY YLIEKSQNQQ EVNEKDLLAL DKWTNLWNWF DISKWLWYIK IFIMIVGGLI GLRIIFAVLS VINRVRQGYP PVSFQTLTPN PRELDRPGGI EEGDGELGKT RSIRLVGGFL ALFWDDLRSL CLFSYHRLRD FSLIAARILE LLGHNSLKGL RLGWEGLKYL GNLLLYWGRE LKNSAVNLVD TIAIVVAGWT DRVIEVLQGI GRAFLHIPRR IRQGLERALL

-
Macromolecule #2: Immunoglobulin G PGT151 Fab, Heavy chain

MacromoleculeName: Immunoglobulin G PGT151 Fab, Heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF ...String:
RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DK

-
Macromolecule #3: Immunoglobulin G PGT151, Light chain

MacromoleculeName: Immunoglobulin G PGT151, Light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

-
Macromolecule #4: Immunoglobulin G PCT64_13C Fab, Heavy chain

MacromoleculeName: Immunoglobulin G PCT64_13C Fab, Heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCAASGFTFT NAWLDWVRQA PGKGLEWVGR IKSKTDGGTT DHAAPVKGRF TISRDDSKNT VYLQMNSLKI EDTAVYYCTT GVETYDFWSG YDDHYYDYYF KDVWGKGTTV TVSS

-
Macromolecule #5: Immunoglobulin G PCT64_13C, Light chain

MacromoleculeName: Immunoglobulin G PCT64_13C, Light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS NNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQSARSFTFG PGTKVDIK

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate
GridMaterial: COPPER / Pretreatment - Type: PLASMA CLEANING

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 222 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 2395
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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