[English] 日本語
Yorodumi
- PDB-5ius: Crystal structure of human PD-L1 in complex with high affinity PD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ius
TitleCrystal structure of human PD-L1 in complex with high affinity PD-1 mutant
Components
  • Programmed cell death 1 ligand 1
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / immune checkpoint / tumor surveillance / cancer / receptor
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 immune response / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of activated T cell proliferation ...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 immune response / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of activated T cell proliferation / negative regulation of interleukin-10 production / negative regulation of T cell activation / humoral immune response / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / regulation of immune response / negative regulation of T cell receptor signaling pathway / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / positive regulation of T cell proliferation / PD-L1(CD274) glycosylation and translocation to plasma membrane / negative regulation of inflammatory response / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / recycling endosome membrane / SPOP-mediated proteasomal degradation of PD-L1(CD274) / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / signaling receptor activity / early endosome membrane / Potential therapeutics for SARS / adaptive immune response / cell surface receptor signaling pathway / transcription coactivator activity / nuclear speck / immune response / receptor ligand activity / external side of plasma membrane / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Programmed cell death protein 1 / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Programmed cell death protein 1 / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.889 Å
AuthorsPascolutti, R. / Sun, X. / Kao, J. / Maute, R. / Ring, A.M. / Bowman, G.R. / Kruse, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP5OD021345 United States
CitationJournal: Structure / Year: 2016
Title: Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant.
Authors: Pascolutti, R. / Sun, X. / Kao, J. / Maute, R.L. / Ring, A.M. / Bowman, G.R. / Kruse, A.C.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 1
B: Programmed cell death protein 1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9275
Polymers79,8924
Non-polymers351
Water59433
1
A: Programmed cell death protein 1
C: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9813
Polymers39,9462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-18 kcal/mol
Surface area18440 Å2
MethodPISA
2
B: Programmed cell death protein 1
D: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)39,9462
Polymers39,9462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-8 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.851, 86.851, 111.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Programmed cell death protein 1 / hPD-1


Mass: 14175.635 Da / Num. of mol.: 2
Mutation: V64H, N66V, Y68H, M70E, N74G, K78T, C93A, L122V, A125V, A132I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Plasmid: pMAL / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#2: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 25770.248 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 / Plasmid: pET28 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 0.1 M bis-TRIS pH 6.4, 17% PEG MME 5000, 2 mM LiCl

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.889→50 Å / Num. obs: 18559 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rsym value: 0.165 / Net I/σ(I): 8.37
Reflection shellResolution: 2.889→3.08 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 0.55 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ, 3SBW

3rrq

3sbw


Resolution: 2.889→47.02 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 1847 9.95 %
Rwork0.2075 --
obs0.2127 18559 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.889→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 1 33 5114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035204
X-RAY DIFFRACTIONf_angle_d0.5687094
X-RAY DIFFRACTIONf_dihedral_angle_d9.9611850
X-RAY DIFFRACTIONf_chiral_restr0.021825
X-RAY DIFFRACTIONf_plane_restr0.002919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8886-2.96670.4641370.39781222X-RAY DIFFRACTION96
2.9667-3.0540.39061440.35371271X-RAY DIFFRACTION99
3.054-3.15250.39541420.34951303X-RAY DIFFRACTION100
3.1525-3.26520.37991390.3191260X-RAY DIFFRACTION100
3.2652-3.39590.35381440.291300X-RAY DIFFRACTION100
3.3959-3.55040.34661410.27541287X-RAY DIFFRACTION100
3.5504-3.73750.34021440.26421292X-RAY DIFFRACTION100
3.7375-3.97160.29731390.23451295X-RAY DIFFRACTION100
3.9716-4.2780.24321400.20771281X-RAY DIFFRACTION100
4.278-4.70820.20141440.15821300X-RAY DIFFRACTION100
4.7082-5.38860.19771430.15281295X-RAY DIFFRACTION100
5.3886-6.78580.21991440.18181299X-RAY DIFFRACTION100
6.7858-47.02580.22941460.16951307X-RAY DIFFRACTION99
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)
18.16432.76533.57225.26042.60437.02250.11220.05820.3130.05330.2363-0.11560.13090.2011-0.21940.64040.10120.10270.90550.00780.7286-40.9259-12.1161-30.8789
22.6218-1.99083.076710.0512-1.14685.95752.06041.30271.26941.124-0.2205-1.66081.26911.1973-1.28191.43930.3206-0.25870.95230.05641.0908-35.2178-24.1369-25.6139
35.9798-1.8063.69765.4701-0.33338.4284-0.24060.3112-0.0401-0.17680.01490.01220.9216-0.22980.38650.853-0.18690.09040.7103-0.07820.5769-42.3023-17.5494-31.554
42.4911-0.1043.82296.26822.57457.34430.1011-0.00270.6370.0738-0.30940.5247-0.5576-0.38980.13410.44290.09030.03080.64710.08010.5777-43.3398-9.9098-29.112
53.1733.0531-3.25035.2525-1.58946.51870.34471.15590.46051.1475-0.6371-0.0392-1.7174-0.35670.13481.53130.2165-0.18030.75530.01770.8038-32.5549-4.861923.2841
60.8178-1.4065-1.90094.39443.99824.65180.8785-0.9073-1.50125.1682-0.4871.62194.6305-4.3781-0.73482.4578-0.3682-0.0661.92090.19881.2209-43.9853-19.229124.8224
75.33711.76814.42636.30690.22386.1702-0.42360.01190.109-0.34630.3602-0.0335-0.1782-0.0085-0.08450.93120.2173-0.06170.890.11420.7344-30.7693-12.808417.1195
82.450.0277-0.91653.05474.64487.4968-1.25050.29560.3638-2.72422.36081.2246-1.60563.4854-0.18411.3488-0.2932-0.13051.68540.59671.3564-19.2354-3.004414.3227
91.63560.072.39283.93632.20777.75010.07550.02340.36951.4590.16380.3959-0.1914-1.2843-0.25561.02930.3117-0.10261.02120.090.7797-41.6536-10.854816.5864
108.83370.80652.05758.86031.4567.8638-1.6675-2.47410.77390.6620.1475-0.3552-2.53281.37841.23262.01470.0135-0.45331.2350.20211.4944-22.32913.988518.5977
113.57161.99211.20438.07983.50636.01120.00250.0741-0.13740.0190.2838-1.2888-0.42021.4948-0.16360.4922-0.0691-0.07151.05650.00740.799-26.1362-1.9076-15.3944
121.7009-3.6337-0.12888.89972.66915.3176-0.4626-0.24980.8332-0.52181.2948-1.3613-2.54641.2354-0.41.3379-0.3482-0.06770.4426-0.04650.9196-40.08522.09610.0812
137.536-3.1682-1.6157.19975.79684.86720.19870.8950.5465-1.041-0.15520.2143-1.6995-0.9435-0.37091.29260.2751-0.04290.73610.20360.7829-46.87325.7613-1.2646
144.0727-3.39991.58976.72064.3369.04920.056-0.35810.4107-0.6066-0.4235-0.062-2.4984-0.58940.2711.8958-0.0667-0.01960.77040.13010.9021-47.115828.91566.9341
158.37830.87813.01946.35120.01369.85611.21170.1762-0.7232-0.15730.0765-0.17130.23940.5423-1.45760.69540.26240.10551.0544-0.00180.7101-63.028914.2051-21.2012
167.89-3.22252.63387.16880.15687.74110.59430.1631-0.1427-0.57050.10650.83471.0816-0.1592-0.38450.5251-0.110.03540.85740.19460.7549-44.2243-8.186-2.9492
178.3769-2.05945.38179.2819-4.15874.6460.116-0.3734-1.3127-0.37210.97111.27561.7636-0.3241-0.87271.19590.1052-0.1950.9954-0.00040.8754-44.3211-19.04462.9114
183.4757-2.8803-1.22885.7733-1.63853.53290.0252-0.466-3.0126-0.44060.47062.86211.6431-3.2633-0.67331.3415-0.2522-0.24281.57640.26611.9321-52.9377-21.57116.0713
193.75161.23231.77248.5754-4.27223.6793-0.94880.6853-0.8484-0.00751.66692.5160.4216-2.6105-0.59731.2687-0.1234-0.08741.46520.2911.5703-58.2691-16.66281.6123
209.5334-6.1989-0.0345.846-0.19367.05130.19782.0775-2.063-1.69650.20952.1512.570.3025-0.54161.46620.0346-0.27871.2421-0.18590.9651-45.8556-20.4264-4.4777
213.4889-0.06392.34783.84941.98547.35730.29110.78960.261-0.9075-0.07270.54320.0116-0.2453-0.07710.74660.08940.05690.66380.12830.9444-48.8449-11.57043.0587
223.568-6.08981.42554.3077-2.82134.81740.88841.888-0.0475-0.3705-0.98750.3481.2540.497-0.32460.87950.058-0.13651.02360.29640.952-49.7712-2.108-2.4673
233.7616-1.59110.50115.9901-4.33735.8303-0.2645-0.85580.28620.56780.57180.4105-1.2178-0.8348-0.30140.73770.25010.02390.7303-0.12920.5386-67.928419.057-17.8982
245.7702-2.26232.38688.2138-3.67667.6091-0.2837-0.3841-0.54850.5357-0.03790.5162-0.6147-0.32310.04710.65530.22970.00571.1688-0.06620.7504-66.532615.1822-13.7241
254.11472.50925.23711.15193.46217.5898-0.61330.88730.6518-0.43850.60660.9253-2.3025-0.1113-0.08211.3193-0.0238-0.0531.04120.13810.935-45.78521.47357.958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 147 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 62 )
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 110 )
8X-RAY DIFFRACTION8chain 'B' and (resid 111 through 118 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 139 )
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 147 )
11X-RAY DIFFRACTION11chain 'C' and (resid 18 through 120 )
12X-RAY DIFFRACTION12chain 'C' and (resid 121 through 159 )
13X-RAY DIFFRACTION13chain 'C' and (resid 160 through 190 )
14X-RAY DIFFRACTION14chain 'C' and (resid 191 through 213 )
15X-RAY DIFFRACTION15chain 'C' and (resid 214 through 231 )
16X-RAY DIFFRACTION16chain 'D' and (resid 18 through 35 )
17X-RAY DIFFRACTION17chain 'D' and (resid 36 through 61 )
18X-RAY DIFFRACTION18chain 'D' and (resid 62 through 73 )
19X-RAY DIFFRACTION19chain 'D' and (resid 74 through 88 )
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 101 )
21X-RAY DIFFRACTION21chain 'D' and (resid 102 through 120 )
22X-RAY DIFFRACTION22chain 'D' and (resid 121 through 137 )
23X-RAY DIFFRACTION23chain 'D' and (resid 138 through 177 )
24X-RAY DIFFRACTION24chain 'D' and (resid 178 through 213 )
25X-RAY DIFFRACTION25chain 'D' and (resid 214 through 229 )

+
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