[English] 日本語
Yorodumi
- PDB-4zqk: Structure of the complex of human programmed death-1 (PD-1) and i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zqk
TitleStructure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.
Components
  • Programmed cell death 1 ligand 1
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / complex / co-stimulation / receptor-ligand complex
Function / homology
Function and homology information


regulatory T cell apoptotic process / negative regulation of tolerance induction / 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 / TRIF-dependent toll-like receptor signaling pathway / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / B cell apoptotic process ...regulatory T cell apoptotic process / negative regulation of tolerance induction / 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 / TRIF-dependent toll-like receptor signaling pathway / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / B cell apoptotic process / positive regulation of T cell apoptotic process / STAT3 nuclear events downstream of ALK signaling / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of T cell activation / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / humoral immune response / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell receptor signaling pathway / regulation of immune response / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / positive regulation of T cell proliferation / negative regulation of inflammatory response / recycling endosome membrane / transmembrane signaling receptor activity / actin cytoskeleton / signaling receptor activity / cellular response to lipopolysaccharide / early endosome membrane / Potential therapeutics for SARS / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / receptor ligand activity / external side of plasma membrane / apoptotic process / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
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 / molecular replacement / Resolution: 2.45 Å
AuthorsZak, K.M. / Dubin, G. / Holak, T.A.
CitationJournal: Structure / Year: 2015
Title: Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1.
Authors: Zak, K.M. / Kitel, R. / Przetocka, S. / Golik, P. / Guzik, K. / Musielak, B. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionMay 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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 1.4Oct 16, 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 1 ligand 1
B: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3863
Polymers26,3632
Non-polymers231
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.862, 70.862, 114.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 13134.085 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZQ7
#2: Protein Programmed cell death protein 1 / hPD-1


Mass: 13228.716 Da / Num. of mol.: 1 / Fragment: UNP Residues 33-150 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15116
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91843 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91843 Å / Relative weight: 1
ReflectionResolution: 2.45→61.37 Å / Num. obs: 12737 / % possible obs: 99.98 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.22
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.21 / % possible all: 99.92

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A -3BIK, chain B 3RRQ

3bik

3rrq


Resolution: 2.45→61.37 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2392 / WRfactor Rwork: 0.2009 / FOM work R set: 0.8095 / SU B: 16.316 / SU ML: 0.175 / SU R Cruickshank DPI: 0.2862 / SU Rfree: 0.2339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 625 4.9 %RANDOM
Rwork0.2071 ---
obs0.2092 12082 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.62 Å2 / Biso mean: 57.568 Å2 / Biso min: 31.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å2-0 Å2
2---0.72 Å20 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 2.45→61.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 1 15 1666
Biso mean--50.06 59.49 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191684
X-RAY DIFFRACTIONr_bond_other_d0.0010.021535
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9512296
X-RAY DIFFRACTIONr_angle_other_deg0.8633514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.675218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54424.92567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36615254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.728155
X-RAY DIFFRACTIONr_chiral_restr0.10.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_mcbond_it3.2314.015881
X-RAY DIFFRACTIONr_mcbond_other3.2334.015880
X-RAY DIFFRACTIONr_mcangle_it4.8856.0111096
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 49 -
Rwork0.225 863 -
all-912 -
obs--99.89 %
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)
13.12471.15810.45261.9953-0.26081.5961-0.13160.00090.0248-0.1420.04720.0077-0.0151-0.05670.08440.2385-0.0829-0.01510.03940.01020.0139-9.754145.1745114.2792
22.353-0.1853-0.75613.211.67452.4375-0.01950.1309-0.11840.2490.0563-0.10490.35380.5131-0.03680.16110.0465-0.05630.2330.0150.043311.871250.2693104.1425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 132
2X-RAY DIFFRACTION2B33 - 146

+
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