[English] 日本語
Yorodumi
- PDB-3bis: Crystal Structure of the PD-L1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bis
TitleCrystal Structure of the PD-L1
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / CO-STIMULATION / IMMUNOGLOBULIN-LIKE BETA-SANDWICH / T CELL / B CELL / PROGRAMMED DEATH / TRANSMEMBRANE / INHIBITORY RECEPTOR / Glycoprotein / Immunoglobulin domain
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 / transcription coactivator activity / adaptive immune response / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.64 Å
AuthorsLin, D.Y. / Tanaka, Y. / Iwasaki, M. / Gittis, A.G. / Su, H.P. / Mikami, B. / Okazaki, T. / Honjo, T. / Minato, N. / Garboczi, D.N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors.
Authors: Lin, D.Y. / Tanaka, Y. / Iwasaki, M. / Gittis, A.G. / Su, H.P. / Mikami, B. / Okazaki, T. / Honjo, T. / Minato, N. / Garboczi, D.N.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
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


Theoretical massNumber of molelcules
Total (without water)50,7942
Polymers50,7942
Non-polymers00
Water81145
1
A: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)25,3971
Polymers25,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)25,3971
Polymers25,3971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.08, 92.70, 141.72
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

-
Components

#1: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / PD-L1 / PDCD1 ligand 1 / B7 homolog 1 / B7-H1 / CD274 antigen


Mass: 25396.779 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q9NZQ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1 M NaCacodylate, 0.2 M ammonium formate or ammonium fluoride, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0722, 0.97948, 1.54
DetectorType: SBC-3 / Detector: CCD / Date: Dec 8, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
20.979481
31.541
ReflectionResolution: 2.64→50 Å / Num. obs: 14169 / % possible obs: 95.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.8
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.272

-
Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.64→19.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 30.871 / SU ML: 0.327 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 700 5 %RANDOM
Rwork0.217 ---
obs0.22 13406 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.64→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 0 45 3457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9594729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13224.819166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07515626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9591520
X-RAY DIFFRACTIONr_chiral_restr0.110.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022600
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22228
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8111.52187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11723466
X-RAY DIFFRACTIONr_scbond_it1.69931471
X-RAY DIFFRACTIONr_scangle_it2.6124.51263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 34 -
Rwork0.384 700 -
obs--69.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.3033-1.30331.37423.5499-0.86572.14780.1415-0.0182-0.1233-0.1094-0.11850.1844-0.0595-0.0421-0.05750.1126-0.01690.01070.1359-0.00150.1657-12.0616.973-33.413
23.9277-0.00531.75114.9149-4.200810.24870.14490.3369-0.4818-0.4355-0.36890.21590.2301-0.4711-0.54050.1640.08340.02160.15480.15750.1514-4.279-16.768-1.858
32.32811.75450.462313.0841-1.67822.2620.0968-0.25170.1548-0.25910.07250.62311.1918-0.0425-0.05820.18190.0350.11180.1204-0.02350.188-21.23523.954-24.4
43.4650.5513-1.93026.3896-2.59216.09890.6055-0.0354-0.5701-0.1398-0.1930.8604-0.1609-0.38480.41520.176-0.15640.04340.18220.03370.2483-27.565-15.083-13.828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA133 - 230116 - 213
2X-RAY DIFFRACTION2AA19 - 1292 - 112
3X-RAY DIFFRACTION3BB133 - 229116 - 212
4X-RAY DIFFRACTION4BB18 - 1291 - 112

+
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://pdbjlvh1.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