[English] 日本語
Yorodumi
- EMDB-24065: CryoEM map of monoclonal antibody Fab DH1025.1 bound to bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24065
TitleCryoEM map of monoclonal antibody Fab DH1025.1 bound to bound to CH505.M5 SOSIP trimer
Map dataCryoEM map of DH1025.1 bound to CH505.M5 SOSIP trimer
Sample
  • Complex: DH1025.1 Fab bound to CH505.M5 SOSIP trimer
    • Protein or peptide: CH505.M5 gp120
    • Protein or peptide: CH505.M5 gp41
    • Protein or peptide: DH1025.1 Fab Heavy Chain
    • Protein or peptide: DH1025.1 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsManne K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI44371 United States
CitationJournal: To Be Published
Title: HIV-1 vaccine induction of protective tier 2 neutralizing antibodies in nonhuman primates is augmented by TLR7/8 agonism
Authors: Tilahun K / Haynes BF
History
DepositionMay 15, 2021-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateAug 17, 2022-
Current statusAug 17, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_24065.png

Downloads & links

-
Map

FileDownload / File: emd_24065.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of DH1025.1 bound to CH505.M5 SOSIP trimer
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.966
Minimum - Maximum-0.3122257 - 1.981716
Average (Standard dev.)0.0040104007 (±0.11686821)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : DH1025.1 Fab bound to CH505.M5 SOSIP trimer

EntireName: DH1025.1 Fab bound to CH505.M5 SOSIP trimer
Components
  • Complex: DH1025.1 Fab bound to CH505.M5 SOSIP trimer
    • Protein or peptide: CH505.M5 gp120
    • Protein or peptide: CH505.M5 gp41
    • Protein or peptide: DH1025.1 Fab Heavy Chain
    • Protein or peptide: DH1025.1 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: DH1025.1 Fab bound to CH505.M5 SOSIP trimer

SupramoleculeName: DH1025.1 Fab bound to CH505.M5 SOSIP trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

-
Macromolecule #1: CH505.M5 gp120

MacromoleculeName: CH505.M5 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 50.965219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV ...String:
ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV SFDPIPIHYC APAGYAILKC NNKTFTGTGP CNNVSTVQCT HGIKPVVSTQ LLLNGSLAEG EIIIRSENIT KN VKTIIVH LNESVKIECT RPNNKTRTSI RIGPGQAFYA TGQVIGDIRE AYCNINESKW NETLQRVSKK LKEYFPHKNI TFQ PSSGGD LEITTHSFNC GGEFFYCNTS SLFNRTYMAN NSTRTITIHC RIKQIINMWQ EVGRAMYAPP IAGNITCISN ITGL LLTRD YGKNNTETFR PGGGNMKDNW RSELYKYKVV KIEPLGVAPT RCKRRVV

-
Macromolecule #2: CH505.M5 gp41

MacromoleculeName: CH505.M5 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 11.238608 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICCTNVP WNSSWSNRNL SEIWDNMTWL QWDKEISNYT QIIYGLLEES QNQQEKNEQ DLLALD

-
Macromolecule #3: DH1025.1 Fab Heavy Chain

MacromoleculeName: DH1025.1 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.238191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLQESGPG LVKPSETLSL TCAVSGGSVS YYNWWSWIRQ PPGKGLEWIG YISGSSGNTY YSPSLKSRVT ISTDTSKNQF SLRLSSVTA ADTAVYYCAS VLQYLDWVLP DRVGEVHWFD VWGPGVLVSV SSASTKGPSV FPLAPSSRST SESTAALGCL V KDYFPEPV ...String:
QVHLQESGPG LVKPSETLSL TCAVSGGSVS YYNWWSWIRQ PPGKGLEWIG YISGSSGNTY YSPSLKSRVT ISTDTSKNQF SLRLSSVTA ADTAVYYCAS VLQYLDWVLP DRVGEVHWFD VWGPGVLVSV SSASTKGPSV FPLAPSSRST SESTAALGCL V KDYFPEPV TVSWNSGSLT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYVCNVNH KPSNTKVDKR VEIKTCGG

-
Macromolecule #4: DH1025.1 Fab Light Chain

MacromoleculeName: DH1025.1 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.12957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ISCQASQGIS SRLAWYQQRP GKAPKLLIHT ASSLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHHSHPLTFG GGTKVEIKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGVLKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ISCQASQGIS SRLAWYQQRP GKAPKLLIHT ASSLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHHSHPLTFG GGTKVEIKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGVLKTGNS Q ESVTEQDS KDNTYSLSST LTLSNTDYQS HNVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: Blot for 2.5 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.15 K / Max: 93.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3056 / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 200000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model


PDB Unreleased entry

PDB-7mw9:
CryoEM structure of monoclonal antibody Fab DH1025.1 bound to bound to CH505.M5 SOSIP trimer

+
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://pdbjlvh1.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