[English] 日本語
Yorodumi
- PDB-9avo: The crystal structure of an engineered Protein GD with Human Kappa Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9avo
TitleThe crystal structure of an engineered Protein GD with Human Kappa Fab
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
  • Protein GD
KeywordsIMMUNE SYSTEM/Chaperone / Fab / Antibody / Protein G / Immunoglobulin Binding Protein / ASF1 / IMMUNE SYSTEM-Chaperone complex
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / protein modification process / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / regulation of transcription by RNA polymerase II / chromatin / nucleus / cytosol
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone
Similarity search - Domain/homology
Histone chaperone ASF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSlezak, T. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117372 United States
CitationJournal: Protein Sci. / Year: 2025
Title: Engineered protein G variants for multifunctional antibody-based assemblies.
Authors: Slezak, T. / O'Leary, K.M. / Li, J. / Rohaim, A. / Davydova, E.K. / Kossiakoff, A.A.
History
DepositionMar 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Fab Heavy Chain
D: Fab Light Chain
A: Histone chaperone ASF1
C: Protein GD


Theoretical massNumber of molelcules
Total (without water)73,2064
Polymers73,2064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-39 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.971, 134.971, 339.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Antibody Fab Heavy Chain


Mass: 24177.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#2: Antibody Fab Light Chain


Mass: 23397.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 18516.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1, CIA1, YJL115W, J0755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32447
#4: Protein Protein GD


Mass: 7113.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Sodium cacodylate pH 6.8 and 0.8M Sodium citrate tribasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→86.73 Å / Num. obs: 31838 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 80.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.049 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 13 % / Num. unique obs: 4540 / CC1/2: 0.879 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→86.73 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1619 5.1 %
Rwork0.2145 --
obs0.2158 31735 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→86.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4912 0 0 0 4912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01730
X-RAY DIFFRACTIONf_angle_d1.28690
X-RAY DIFFRACTIONf_dihedral_angle_d6.469691
X-RAY DIFFRACTIONf_chiral_restr0.067791
X-RAY DIFFRACTIONf_plane_restr0.012873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.43631130.38922465X-RAY DIFFRACTION99
3.09-3.190.41281380.35172452X-RAY DIFFRACTION100
3.19-3.30.36631430.34392465X-RAY DIFFRACTION99
3.3-3.430.33141230.29372467X-RAY DIFFRACTION99
3.43-3.590.28981330.25542479X-RAY DIFFRACTION100
3.59-3.780.23751210.23992505X-RAY DIFFRACTION100
3.78-4.020.30091510.22922495X-RAY DIFFRACTION100
4.02-4.330.16911380.1842516X-RAY DIFFRACTION100
4.33-4.760.17931130.14362513X-RAY DIFFRACTION99
4.76-5.450.18111380.15442540X-RAY DIFFRACTION100
5.45-6.870.24651320.19842556X-RAY DIFFRACTION99
6.87-86.730.21511760.20192663X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.2028 Å / Origin y: -8.148 Å / Origin z: 25.401 Å
111213212223313233
T0.8735 Å2-0.0042 Å2-0.1767 Å2-0.5093 Å2-0.0022 Å2--0.8233 Å2
L1.5043 °2-0.0279 °2-0.3516 °2-0.7522 °20.0459 °2--3.0029 °2
S-0.0306 Å °-0.0721 Å °0.009 Å °0.425 Å °0.1165 Å °-0.1194 Å °0.2593 Å °0.7983 Å °-0.0826 Å °
Refinement TLS groupSelection details: all

+
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