[English] 日本語
Yorodumi
- PDB-7xae: Crystal strucutre of PD-L1 and 3ONJA protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xae
TitleCrystal strucutre of PD-L1 and 3ONJA protein
Components
  • 2IC6
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / receptor ligand activity / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
chemical production metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsLiu, K.F. / Xu, Z.P. / Han, P. / Gao, G.F. / Chai, Y. / Tan, S.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169208 China
CitationJournal: To Be Published
Title: Crystal strucutre of PD-L1 and 2IC6 protein
Authors: Liu, K.F. / Xu, Z.P. / Han, P. / Gao, G.F. / Chai, Y. / Tan, S.G.
History
DepositionMar 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
C: 2IC6
D: 2IC6


Theoretical massNumber of molelcules
Total (without water)73,9834
Polymers73,9834
Non-polymers00
Water00
1
A: Programmed cell death 1 ligand 1
D: 2IC6


Theoretical massNumber of molelcules
Total (without water)36,9912
Polymers36,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-9 kcal/mol
Surface area17350 Å2
MethodPISA
2
B: Programmed cell death 1 ligand 1
C: 2IC6


Theoretical massNumber of molelcules
Total (without water)36,9912
Polymers36,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-9 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.079, 103.079, 173.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 27482.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Protein 2IC6


Mass: 9509.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) chemical production metagenome (others)
Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.43→50 Å / Num. obs: 12131 / % possible obs: 82.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.47 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 18.797
Reflection shellResolution: 3.43→3.55 Å / Rmerge(I) obs: 2.045 / Num. unique obs: 12131

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13-2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ

3rrq


Resolution: 3.44→44.56 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2617 486 4.88 %
Rwork0.2481 9467 -
obs0.2488 9953 82.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.47 Å2
Refinement stepCycle: LAST / Resolution: 3.44→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 0 0 4616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254688
X-RAY DIFFRACTIONf_angle_d0.64276349
X-RAY DIFFRACTIONf_chiral_restr0.0448752
X-RAY DIFFRACTIONf_plane_restr0.0051809
X-RAY DIFFRACTIONf_dihedral_angle_d16.26531777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.44-3.930.26541020.28191799X-RAY DIFFRACTION47.55
3.93-4.950.29441910.2443817X-RAY DIFFRACTION100
4.96-44.560.22561930.23553851X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / 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)
10.007531196245380.01136019259940.00354918405034-0.00131272222556-0.05972128058280.00186454929605-0.0564231779344-0.05219238771510.07489467818590.0698933931440.14198604714-0.07703649686190.02923768016570.1279789000110.1169215971070.08484406754180.01905694998980.09398331275850.2942038093150.6866837349180.039075030882515.298147298-23.1772834782-13.7558800958
20.00860784568144-0.002994057716-0.003032274888980.00351356705849-0.0425247425698-0.00160936738051-0.0664266091210.0307610618622-0.026916720949-0.0825875133520.104438596129-0.0818072555797-0.01447768984980.1053777947910.08392242643860.09827840270880.0268299644283-0.1013197033580.2877064743830.6740994929290.09518620709915.2606385237-28.3599395559-29.9351937944
30.0362982422771-0.03917156276160.01299302380350.0402084437420.0002317471356740.0510771006741-0.07876680728920.008913972512030.01464962500270.0359184382705-0.05189481885530.003874645556940.0170289402983-0.0149572108322-0.133044724956-0.03292503200950.00679659745781-0.06216522827380.1603753270760.1477468889140.208694215285-33.2012941838-31.1414667174-33.3865511424
40.111558437785-0.009779886210180.03224004749030.06072742686380.06653936970260.148597840797-0.0747658490230.005180266243740.0156683890538-0.0261571163517-0.05770448213310.0392792523827-0.0291645244774-0.0678057770144-0.08372568548770.02270082786580.02319003971320.0279351939680.1826028053190.1030119484220.268374285758-33.2181392621-20.4413140015-10.3189115222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA18 - 2291 - 212
22chain BBB18 - 2291 - 212
33chain CCC3 - 791 - 77
44chain DDD3 - 791 - 77

+
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