[English] 日本語
Yorodumi
- PDB-7jlk: Crystal structure of glVRC01 Fab in complex with anti-idiotype iv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jlk
TitleCrystal structure of glVRC01 Fab in complex with anti-idiotype iv1 scFv
Components
  • glVRC01 Heavy Chain
  • glVRC01 Light Chain
  • iv1 Heavy Chain
  • iv1 Light Chain
KeywordsIMMUNE SYSTEM / iv1 / glVRC01 / Fab / scFv / HIV-1 / anti-idiotype
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWeidle, C. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2021
Title: Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies.
Authors: Seydoux, E. / Wan, Y.H. / Feng, J. / Wall, A. / Aljedani, S. / Homad, L.J. / MacCamy, A.J. / Weidle, C. / Gray, M.D. / Brumage, L. / Taylor, J.J. / Pancera, M. / Stamatatos, L. / McGuire, A.T.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: iv1 Heavy Chain
A: glVRC01 Heavy Chain
B: glVRC01 Light Chain
L: iv1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,32544
Polymers75,6594
Non-polymers1,66640
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex was further purified by size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.019, 85.244, 113.636
Angle α, β, γ (deg.)90.000, 99.733, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11H-370-

HOH

21B-550-

HOH

-
Components

-
Antibody , 4 types, 4 molecules HABL

#1: Antibody iv1 Heavy Chain


Mass: 14582.077 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody glVRC01 Heavy Chain


Mass: 25319.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 / Production host: Homo sapiens (human)
#3: Antibody glVRC01 Light Chain


Mass: 23019.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody iv1 Light Chain


Mass: 12738.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Non-polymers , 5 types, 522 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.0, PEG 8000 / Temp details: room temperture

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 44594 / % possible obs: 99.15 % / Redundancy: 1.7 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.911 / Net I/σ(I): 4
Reflection shellResolution: 1.99→2.07 Å / Num. unique obs: 4230 / CC1/2: 0.822

-
Processing

Software
NameVersionClassification
PHASER1.15.2_3472phasing
PHENIX1.15.2_3472refinement
Cootmodel building
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 1.99→42.62 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 2272 5.1 %
Rwork0.1791 42308 -
obs0.182 44580 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.67 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 82 482 5638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025237
X-RAY DIFFRACTIONf_angle_d0.50597102
X-RAY DIFFRACTIONf_chiral_restr0.0429783
X-RAY DIFFRACTIONf_plane_restr0.003910
X-RAY DIFFRACTIONf_dihedral_angle_d11.27943084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.30261170.26692414X-RAY DIFFRACTION90.17
2.04-2.080.31241360.27262619X-RAY DIFFRACTION98.92
2.08-2.140.29871450.242652X-RAY DIFFRACTION99.33
2.14-2.190.30151650.23662623X-RAY DIFFRACTION99.36
2.19-2.260.27621320.2342625X-RAY DIFFRACTION99.64
2.26-2.330.32691330.22382654X-RAY DIFFRACTION99.57
2.33-2.420.26681450.20482692X-RAY DIFFRACTION99.96
2.42-2.510.2911550.21212635X-RAY DIFFRACTION99.75
2.51-2.630.2761510.19612649X-RAY DIFFRACTION99.96
2.63-2.760.26861400.19892665X-RAY DIFFRACTION99.89
2.76-2.940.24741380.18922642X-RAY DIFFRACTION99.93
2.94-3.160.24611340.18592666X-RAY DIFFRACTION99.96
3.16-3.480.25031490.1652672X-RAY DIFFRACTION99.93
3.48-3.990.20451430.14822682X-RAY DIFFRACTION100
3.99-5.020.16231250.13112719X-RAY DIFFRACTION100
5.02-42.620.21171640.17642699X-RAY DIFFRACTION99.72

+
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