[English] 日本語
Yorodumi
- PDB-6xoc: Crystal structure of glVRC01 Fab in complex with anti-idiotypic i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xoc
TitleCrystal structure of glVRC01 Fab in complex with anti-idiotypic iv4 Fab
Components
  • (iGL-VRC01 Fab ...) x 2
  • IV4 Fab Light Chain
  • Iv4 Fab Heavy Chain
KeywordsIMMUNE SYSTEM / Fab / Complex / HIV / CD4-binding site
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAljedani, S.S. / Weidle, 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 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
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 1.3Nov 6, 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
A: Iv4 Fab Heavy Chain
B: IV4 Fab Light Chain
H: iGL-VRC01 Fab Heavy Chain
L: iGL-VRC01 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,62821
Polymers94,4534
Non-polymers1,17417
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-35 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.016, 114.417, 220.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Components on special symmetry positions
IDModelComponents
11H-1226-

HOH

-
Components

-
Antibody , 4 types, 4 molecules ABHL

#1: Antibody Iv4 Fab Heavy Chain


Mass: 23983.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody IV4 Fab Light Chain


Mass: 23897.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody iGL-VRC01 Fab Heavy Chain


Mass: 23841.678 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 iGL-VRC01 Fab Light Chain


Mass: 22730.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 6 types, 247 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 7.5, 8%w/v PEG 20K, 8%w/v PEG MME 550 and 0.2 M KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→110.5 Å / Num. obs: 46804 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.99 / Net I/σ(I): 17
Reflection shellResolution: 2.45→2.54 Å / Num. unique obs: 46727 / CC1/2: 0.785

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACKdata scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 2.45→50.01 Å / SU ML: 0.274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 2188 5.26 %
Rwork0.1986 39403 -
obs0.2008 41591 88.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.27 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 0 71 230 6818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00976732
X-RAY DIFFRACTIONf_angle_d0.99169150
X-RAY DIFFRACTIONf_chiral_restr0.05991018
X-RAY DIFFRACTIONf_plane_restr0.00571174
X-RAY DIFFRACTIONf_dihedral_angle_d20.2532368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.3159730.26261228X-RAY DIFFRACTION45.02
2.51-2.560.4066780.26651566X-RAY DIFFRACTION56.57
2.56-2.630.29181030.23851847X-RAY DIFFRACTION67.4
2.63-2.70.26891160.24092103X-RAY DIFFRACTION77.67
2.7-2.780.30591110.24462330X-RAY DIFFRACTION84.03
2.78-2.870.30531550.2472507X-RAY DIFFRACTION92.05
2.87-2.970.29261310.23352701X-RAY DIFFRACTION97.69
2.97-3.090.28861590.23652743X-RAY DIFFRACTION99.79
3.09-3.230.27131440.22662754X-RAY DIFFRACTION99.97
3.23-3.40.22631480.22032750X-RAY DIFFRACTION100
3.4-3.610.27511690.19722778X-RAY DIFFRACTION99.97
3.61-3.890.22631600.18482760X-RAY DIFFRACTION99.97
3.89-4.280.19261590.16762771X-RAY DIFFRACTION100
4.28-4.90.20781560.14732798X-RAY DIFFRACTION99.97
4.9-6.180.19091670.18052815X-RAY DIFFRACTION100
6.18-50.010.21421590.18942952X-RAY DIFFRACTION99.87

+
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