[English] 日本語
Yorodumi
- PDB-8vte: Co-structure of the Fab of the anti-TIGIT Vibostolimab antibody w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vte
TitleCo-structure of the Fab of the anti-TIGIT Vibostolimab antibody with its antigen
Components
  • T-cell immunoreceptor with Ig and ITIM domains
  • Tiragolumab antibody heavy chain variable domains
  • Tiragolumab antibody light chain variable domains
KeywordsIMMUNE SYSTEM / antibody TIGIT immunotherapy
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsFischmann, T. / Bahmanjah, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Pharmacological and structural characterization of vibostolimab, a novel anti-human TIGIT blocking antibody for cancer immunotherapy
Authors: Fischmann, T.O. / Malashock, D. / Wang, H. / Grein, J. / Bahmanjah, S. / Ban, D. / Chien, E. / Hsieh, M. / Mayhood, T. / Yuan, J. / Beaumont, M. / Baker, J. / McCoy, M.A. / Wilson, D. / ...Authors: Fischmann, T.O. / Malashock, D. / Wang, H. / Grein, J. / Bahmanjah, S. / Ban, D. / Chien, E. / Hsieh, M. / Mayhood, T. / Yuan, J. / Beaumont, M. / Baker, J. / McCoy, M.A. / Wilson, D. / Williams, S.M.G. / Blumenschein, W. / Fayadat-Dilman, L. / Seghezzi, W. / Keenan, T. / Han, J.-H.
History
DepositionJan 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tiragolumab antibody light chain variable domains
B: Tiragolumab antibody heavy chain variable domains
C: Tiragolumab antibody light chain variable domains
D: Tiragolumab antibody heavy chain variable domains
E: T-cell immunoreceptor with Ig and ITIM domains
F: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)124,7156
Polymers124,7156
Non-polymers00
Water7,656425
1
A: Tiragolumab antibody light chain variable domains
B: Tiragolumab antibody heavy chain variable domains
E: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)62,3573
Polymers62,3573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tiragolumab antibody light chain variable domains
D: Tiragolumab antibody heavy chain variable domains
F: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)62,3573
Polymers62,3573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.689, 213.689, 66.428
Angle α, β, γ (deg.)90, 90, 90
Int Tables number79
Space group name H-MI4

-
Components

#1: Antibody Tiragolumab antibody light chain variable domains


Mass: 24246.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Tiragolumab antibody heavy chain variable domains


Mass: 24696.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: 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: 13413.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIGIT, VSIG9, VSTM3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q495A1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02M D-Glucose; 0.02M D-Mannose; 0.02M D-Galactose; 0.02M L-Fucose; 0.02M D-Xylose; 0.02M N-Acetyl-D-Glucosamine; 0.1M Imidazole, 0.1M MES; 20%v/v Glycerol; 10% PEG4K

-
Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→33.21 Å / Num. obs: 49814 / % possible obs: 93.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.6
Reflection shellResolution: 2.29→2.502 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2493 / CC1/2: 0.651

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→33.21 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.456 / SU Rfree Blow DPI: 0.283
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 2483 -RANDOM
Rwork0.2285 ---
obs0.2305 49801 73.5 %-
Displacement parametersBiso mean: 70.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.9623 Å20 Å20 Å2
2--0.9623 Å20 Å2
3----1.9247 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.29→33.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8413 0 0 425 8838
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00716803HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9930305HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4970SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2648HARMONIC5
X-RAY DIFFRACTIONt_it8633HARMONIC10
X-RAY DIFFRACTIONt_nbd12SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion1161SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12324SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion15.61
LS refinement shellResolution: 2.29→2.43 Å
RfactorNum. reflection% reflection
Rfree0.3305 32 -
Rwork0.2845 --
obs0.286 997 9.05 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.26512.2704-0.02293.96740.13773.2102-0.0202-0.01390.3715-0.0139-0.0046-0.08750.3715-0.08750.02470.2291-0.11810.04540.0312-0.0660.050162.9938-41.8512-27.7564
21.592-0.1017-0.61997.40771.46883.0902-0.04830.43560.01940.43560.08850.22240.01940.2224-0.04020.0345-0.0396-0.08230.0945-0.02640.051686.4129-11.7405-25.2925
32.34270.0997-0.18084.78040.50621.4514-0.0297-0.20420.0661-0.2042-0.2061-0.6040.0661-0.6040.23580.1197-0.096-0.00730.2745-0.08730.075647.8976-25.8734-31.4472
43.72810.9445-1.80883.4840.21196.2057-0.0342-0.1561-0.1913-0.1561-0.01380.1367-0.19130.13670.0480.1465-0.0705-0.07130.0065-0.0213-0.004576.6571-9.0091-37.5361
55.6098-0.2274-0.28222.90640.05024.164-0.10280.05580.27590.05580.0023-0.56950.2759-0.56950.10060.2301-0.26440.04570.1657-0.05740.042954.8518-35.96452.6129
66.0879-0.41550.380712.7037-2.68385.61350.0927-1.3219-0.0359-1.32190.2178-0.8299-0.0359-0.8299-0.3105-0.08080.0246-0.01530.4305-0.13150.252431.5876-8.8358-10.4602
71.7243-0.30810.76712.0517-0.6092.41140.0294-0.01230.0696-0.0123-0.0674-0.11470.0696-0.11470.03810.1886-0.12390.03870.1386-0.05650.092269.7529-19.73840.6629
88.7231-0.3058-2.02626.4878-0.26885.81340.12920.8357-0.1540.83570.0421-1.0099-0.154-1.0099-0.17140.16590.03620.11660.2623-0.23160.163141.8768-1.9318-0.3938
914.4761-1.4657-2.05297.7753-1.18987.6927-0.14790.0460.54270.046-0.0699-1.1960.5427-1.1960.2179-0.1614-0.31290.2023-0.0581-0.21470.345828.4355-45.0558-26.2091
1010.23541.81720.00614.92181.19063.0215-0.3434-0.18840.6287-0.18840.2880.19970.62870.19970.05540.1204-0.00350.1253-0.04420.03280.050690.0858-38.98034.7815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|111 }A1 - 111
2X-RAY DIFFRACTION2{ A|112 - A|219 }A112 - 219
3X-RAY DIFFRACTION3{ B|1 - B|127 }B1 - 127
4X-RAY DIFFRACTION4{ B|128 - B|227 }B128 - 227
5X-RAY DIFFRACTION5{ C|1 - C|111 }C1 - 111
6X-RAY DIFFRACTION6{ C|112 - C|217 }C112 - 217
7X-RAY DIFFRACTION7{ D|1 - D|127 }D1 - 127
8X-RAY DIFFRACTION8{ D|128 - D|227 }D128 - 227
9X-RAY DIFFRACTION9{ E|* }E25 - 126
10X-RAY DIFFRACTION10{ F|* }F22 - 128

+
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