[English] 日本語
Yorodumi
- PDB-9dq5: Crystal structure of Anti-CTLA-4 Fab (9D9) in complex with mouse ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dq5
TitleCrystal structure of Anti-CTLA-4 Fab (9D9) in complex with mouse CTLA-4
Components
  • 9D9 heavy chain
  • 9D9 light chain
  • Cytotoxic T-lymphocyte protein 4
KeywordsANTITUMOR PROTEIN/IMMUNE SYSTEM / ANTIBODY / CTLA-4. ANTITUMOR PROTEIN-IMMUNE SYSTEM complex / ANTITUMOR PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Co-inhibition by CTLA4 / Co-stimulation by CD28 / protein complex involved in cell adhesion / regulation of T cell proliferation / adaptive immune response / external side of plasma membrane / plasma membrane
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLee, P.S. / Diong, S.J. / Robison, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2025
Title: Engineered ipilimumab variants that bind human and mouse CTLA-4.
Authors: Robison, B. / Diong, S.J. / Kumar, A. / Moon, T.M. / Chang, O. / Chau, B. / Bee, C. / Barman, I. / Rajpal, A. / Korman, A.J. / West, S. / Strop, P. / Lee, P.S.
History
DepositionSep 23, 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
H: 9D9 heavy chain
L: 9D9 light chain
C: Cytotoxic T-lymphocyte protein 4
I: 9D9 heavy chain
M: 9D9 light chain
D: Cytotoxic T-lymphocyte protein 4
J: 9D9 heavy chain
N: 9D9 light chain


Theoretical massNumber of molelcules
Total (without water)175,9388
Polymers175,9388
Non-polymers00
Water00
1
H: 9D9 heavy chain
L: 9D9 light chain
C: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)63,6563
Polymers63,6563
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 9D9 heavy chain
M: 9D9 light chain
D: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)63,6563
Polymers63,6563
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: 9D9 heavy chain
N: 9D9 light chain


Theoretical massNumber of molelcules
Total (without water)48,6262
Polymers48,6262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.508, 208.841, 91.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Antibody 9D9 heavy chain


Mass: 24612.520 Da / Num. of mol.: 3 / Fragment: Fab heavy chain with hexahistidine tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody 9D9 light chain


Mass: 24013.777 Da / Num. of mol.: 3 / Fragment: Fab light chain with hexahistidine tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 15029.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Expi293F / Gene: Ctla4, Cd152 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P09793
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 15% PEG10000, 0.1 M Bis-Tris, pH 6.5, 0.1 M ammonium acetate

-
Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→208.84 Å / Num. obs: 44164 / % possible obs: 97.2 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 18.1 / Num. measured all: 286219
Reflection shellResolution: 3.1→3.22 Å / % possible obs: 73.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.99 / Num. measured all: 14368 / Num. unique obs: 3442 / CC1/2: 0.618 / Rpim(I) all: 0.501 / Rrim(I) all: 1.118 / Net I/σ(I) obs: 1.1

-
Processing

Software
NameVersionClassification
PHENIX(???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→36.48 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3012 2237 5.08 %
Rwork0.2385 --
obs0.2417 44060 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11258 0 0 0 11258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.182
X-RAY DIFFRACTIONf_dihedral_angle_d15.5913980
X-RAY DIFFRACTIONf_chiral_restr0.0551806
X-RAY DIFFRACTIONf_plane_restr0.0092013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.170.6434810.63031438X-RAY DIFFRACTION54
3.17-3.240.49181550.44422631X-RAY DIFFRACTION100
3.24-3.320.46391520.36412634X-RAY DIFFRACTION100
3.32-3.410.41071370.31012671X-RAY DIFFRACTION100
3.41-3.510.34641440.28532675X-RAY DIFFRACTION100
3.51-3.630.33191300.28722637X-RAY DIFFRACTION100
3.63-3.760.36781600.29622654X-RAY DIFFRACTION100
3.76-3.910.39571380.30852670X-RAY DIFFRACTION100
3.91-4.080.35651360.29022690X-RAY DIFFRACTION100
4.08-4.30.34271320.24252691X-RAY DIFFRACTION100
4.3-4.570.27021350.21692694X-RAY DIFFRACTION100
4.57-4.920.29691380.20372680X-RAY DIFFRACTION100
4.92-5.410.30111370.20292727X-RAY DIFFRACTION100
5.41-6.190.28131510.21392707X-RAY DIFFRACTION100
6.19-7.790.25711400.23682764X-RAY DIFFRACTION100
7.79-36.480.24621710.20272860X-RAY DIFFRACTION100

+
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