[English] 日本語
Yorodumi
- PDB-9dq4: Crystal structure of engineered Ipilimumab (mipi.4) Fab in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dq4
TitleCrystal structure of engineered Ipilimumab (mipi.4) Fab in complex with mouse CTLA-4
Components
  • Cytotoxic T-lymphocyte protein 4
  • mipi.4 heavy chain
  • mipi.4 light chain
KeywordsANTITUMOR PROTEIN/IMMUNE SYSTEM / Antibody / CTLA-4 / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsDiong, S.J. / Lee, P.S.
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
A: Cytotoxic T-lymphocyte protein 4
H: mipi.4 heavy chain
L: mipi.4 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9664
Polymers62,2333
Non-polymers7331
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-22 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.314, 152.778, 48.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13916.556 Da / Num. of mol.: 1
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
#2: Antibody mipi.4 heavy chain


Mass: 24708.742 Da / Num. of mol.: 1
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: Antibody mipi.4 light chain


Mass: 23608.199 Da / Num. of mol.: 1
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)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.25 M sodium acetate trihydrate, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→82.163 Å / Num. obs: 68048 / % possible obs: 86.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.057 / Rrim(I) all: 0.139 / Net I/σ(I): 7.2
Reflection shellResolution: 1.57→1.946 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.675 / Num. unique obs: 2337 / Rpim(I) all: 0.416 / Rrim(I) all: 0.797

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→40.02 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 3449 5.07 %
Rwork0.2048 --
obs0.2062 68048 78.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 49 395 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.257
X-RAY DIFFRACTIONf_dihedral_angle_d15.1091477
X-RAY DIFFRACTIONf_chiral_restr0.075659
X-RAY DIFFRACTIONf_plane_restr0.011723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.2847220.2509401X-RAY DIFFRACTION12
1.59-1.610.2505310.2477578X-RAY DIFFRACTION18
1.61-1.630.3069440.2561911X-RAY DIFFRACTION28
1.63-1.660.2791580.24981202X-RAY DIFFRACTION37
1.66-1.690.2686830.24821543X-RAY DIFFRACTION48
1.69-1.710.27841060.25441985X-RAY DIFFRACTION61
1.71-1.750.27941390.25672483X-RAY DIFFRACTION78
1.75-1.780.24741560.24752858X-RAY DIFFRACTION87
1.78-1.820.28021570.24843125X-RAY DIFFRACTION98
1.82-1.860.27261700.24223259X-RAY DIFFRACTION100
1.86-1.90.25251680.2263241X-RAY DIFFRACTION100
1.9-1.950.2901930.22392516X-RAY DIFFRACTION76
1.95-20.26771400.21133295X-RAY DIFFRACTION100
2-2.050.22091810.21182992X-RAY DIFFRACTION99
2.08-2.120.26051180.20822261X-RAY DIFFRACTION98
2.12-2.20.25882000.20453232X-RAY DIFFRACTION100
2.2-2.290.23881170.21742399X-RAY DIFFRACTION73
2.29-2.390.25891550.20743265X-RAY DIFFRACTION99
2.39-2.520.23091750.20663256X-RAY DIFFRACTION99
2.52-2.680.2251790.21163263X-RAY DIFFRACTION99
2.68-2.880.23881980.21563218X-RAY DIFFRACTION99
2.88-3.170.24091750.21033289X-RAY DIFFRACTION99
3.17-3.630.22462050.19623235X-RAY DIFFRACTION98
3.63-4.570.18121910.16493301X-RAY DIFFRACTION98
4.57-40.020.22051880.18763491X-RAY DIFFRACTION99

+
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