[English] 日本語
Yorodumi
- PDB-8szy: Crystal Structure of Heterotrimeric Anti-TIGIT Fabs in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8szy
TitleCrystal Structure of Heterotrimeric Anti-TIGIT Fabs in complex with human TIGIT
Components
  • BMS-986207 Fab Heavy Chain
  • BMS-986207 light chain
  • CHA.9.543 Fab heavy chain
  • CHA.9.543 light chain
  • T-cell immunoreceptor with Ig and ITIM domains
KeywordsIMMUNE SYSTEM / PROTEIN BINDING / Antibody / TIGIT / PVR-Family
Function / homology
Function and homology information


negative regulation of T cell activation / negative regulation of interleukin-12 production / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-10 production / signaling receptor activity / signaling receptor binding / cell surface / identical protein binding / plasma membrane
Similarity search - Function
T-cell immunoglobulin and ITIM domain receptor / 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
T-cell immunoreceptor with Ig and ITIM domains
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsDiong, S.J. / Lee, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Mabs / Year: 2023
Title: Biophysical characterization of PVR family interactions and therapeutic antibody recognition to TIGIT.
Authors: Diong, S.J. / Jashnani, A. / Drake, A.W. / Bee, C. / Findeisen, F. / Dollinger, G. / Wang, F. / Rajpal, A. / Strop, P. / Lee, P.S.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: CHA.9.543 Fab heavy chain
B: CHA.9.543 light chain
H: BMS-986207 Fab Heavy Chain
L: BMS-986207 light chain
T: T-cell immunoreceptor with Ig and ITIM domains
C: CHA.9.543 Fab heavy chain
D: CHA.9.543 light chain
I: BMS-986207 Fab Heavy Chain
M: BMS-986207 light chain
U: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,15812
Polymers220,71510
Non-polymers4422
Water2,018112
1
A: CHA.9.543 Fab heavy chain
B: CHA.9.543 light chain
H: BMS-986207 Fab Heavy Chain
L: BMS-986207 light chain
T: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5796
Polymers110,3585
Non-polymers2211
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CHA.9.543 Fab heavy chain
D: CHA.9.543 light chain
I: BMS-986207 Fab Heavy Chain
M: BMS-986207 light chain
U: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5796
Polymers110,3585
Non-polymers2211
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.850, 216.910, 109.450
Angle α, β, γ (deg.)90.000, 95.970, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

-
Components

-
Antibody , 4 types, 8 molecules ACBDHILM

#1: Antibody CHA.9.543 Fab heavy chain


Mass: 24309.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CHA.9.543 light chain


Mass: 24072.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody BMS-986207 Fab Heavy Chain


Mass: 25870.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody BMS-986207 light chain


Mass: 23621.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein / Sugars / Non-polymers , 3 types, 116 molecules TU

#5: Protein T-cell immunoreceptor with Ig and ITIM domains / V-set and immunoglobulin domain-containing protein 9 / V-set and transmembrane domain-containing protein 3


Mass: 12483.785 Da / Num. of mol.: 2 / Mutation: C69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIGIT, VSIG9, VSTM3 / Production host: Homo sapiens (human) / References: UniProt: Q495A1
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium phosphate monobasic monohydrate, 20% w/v Polyethylene glycol 1,000

-
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: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.306→108.856 Å / Num. obs: 65410 / % possible obs: 70.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 35.04 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.091 / Rrim(I) all: 0.168 / Net I/σ(I): 7.5
Reflection shellResolution: 2.306→2.479 Å / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3271 / CC1/2: 0.6 / Rpim(I) all: 0.491 / Rrim(I) all: 0.854

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
STARANISOdata scaling
XSCALEdata scaling
Cootmodel building
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→45.6 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.0909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 3191 4.88 %
Rwork0.227 62187 -
obs0.229 65378 70.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.66 Å2
Refinement stepCycle: LAST / Resolution: 2.31→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14751 0 28 112 14891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004915147
X-RAY DIFFRACTIONf_angle_d0.881320659
X-RAY DIFFRACTIONf_chiral_restr0.10082346
X-RAY DIFFRACTIONf_plane_restr0.01442630
X-RAY DIFFRACTIONf_dihedral_angle_d16.09055351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.340.2633280.2909383X-RAY DIFFRACTION10.26
2.34-2.380.3883290.315517X-RAY DIFFRACTION13.5
2.38-2.420.3163330.3151662X-RAY DIFFRACTION17.12
2.42-2.460.3477480.3283976X-RAY DIFFRACTION25.64
2.46-2.50.3817790.32031285X-RAY DIFFRACTION33.93
2.5-2.550.3274760.31931692X-RAY DIFFRACTION43.01
2.55-2.60.34241090.32411913X-RAY DIFFRACTION50.94
2.6-2.660.39291190.31982184X-RAY DIFFRACTION56.92
2.66-2.720.35371490.31942493X-RAY DIFFRACTION64.96
2.72-2.790.32681370.31752812X-RAY DIFFRACTION73.52
2.79-2.860.33111560.30413021X-RAY DIFFRACTION77.45
2.86-2.950.32611830.30043369X-RAY DIFFRACTION89.43
2.95-3.040.3151840.29713801X-RAY DIFFRACTION97.24
3.04-3.150.34121860.29453804X-RAY DIFFRACTION99.58
3.15-3.280.31552050.28613893X-RAY DIFFRACTION99.56
3.28-3.430.32441850.25233772X-RAY DIFFRACTION99.12
3.43-3.610.2811790.22853814X-RAY DIFFRACTION98.69
3.61-3.830.28311520.21422940X-RAY DIFFRACTION75.58
3.83-4.130.24552020.19033740X-RAY DIFFRACTION97.6
4.13-4.550.2021870.15493750X-RAY DIFFRACTION96.8
4.55-5.20.18761710.14913766X-RAY DIFFRACTION97.09
5.2-6.550.21942060.17583809X-RAY DIFFRACTION98.36
6.55-45.60.19941880.19043791X-RAY DIFFRACTION97.31
Refinement TLS params.Method: refined / Origin x: 11.5172330803 Å / Origin y: 39.7083482266 Å / Origin z: -26.4063142197 Å
111213212223313233
T0.0377147752385 Å20.0123720508454 Å2-0.00777820795839 Å2-0.121751130453 Å2-0.00976466635721 Å2--0.11618036816 Å2
L-0.00406046283219 °2-0.0269015134386 °2-0.0411445605458 °2-0.150143361703 °20.158191688689 °2--0.279974593236 °2
S-0.01028216234 Å °-0.00124123420841 Å °0.00464861116361 Å °-0.00142670602003 Å °0.0268035693408 Å °0.0156291612282 Å °-0.00563681411091 Å °-0.00966878573869 Å °-0.0157897420394 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