[English] 日本語
Yorodumi
- PDB-6umt: High-affinity human PD-1 PD-L2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6umt
TitleHigh-affinity human PD-1 PD-L2 complex
Components
  • Programmed cell death 1 ligand 2
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / PD-L2 / immune checkpoint
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / endomembrane system / signaling receptor activity / cellular response to lipopolysaccharide / Potential therapeutics for SARS / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane / apoptotic process / extracellular region / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / : / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Programmed cell death protein 1 / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / : / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.986 Å
AuthorsTang, S. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.
Authors: Tang, S. / Kim, P.S.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 1
B: Programmed cell death 1 ligand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4033
Polymers29,3782
Non-polymers241
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.291, 67.798, 89.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 15429.354 Da / Num. of mol.: 1 / Fragment: UNP residues 33-150 / Mutation: N74G, T76P, A132V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q15116
#2: Protein Programmed cell death 1 ligand 2 / Programmed death ligand 2 / Butyrophilin B7-DC / B7-DC


Mass: 13949.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1LG2, B7DC, CD273, PDCD1L2, PDL2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9BQ51
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM magnesium acetate, 10% w/v PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.986→50 Å / Num. obs: 17793 / % possible obs: 98.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 35.84 Å2 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.051 / Rrim(I) all: 0.155 / Χ2: 2.277 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.99-2.025.70.7617740.7620.3150.8270.53987.7
2.02-2.066.30.6638180.8450.2660.7170.54592
2.06-2.16.70.6368420.8550.2510.6860.59795.7
2.1-2.147.10.5818560.8870.2210.6230.6397.4
2.14-2.197.60.5258860.9150.1950.5620.64299.3
2.19-2.248.10.4978710.9240.180.530.70599.8
2.24-2.380.4579050.9310.1650.4870.76598.8
2.3-2.368.50.4068740.9520.1420.4310.79599.9
2.36-2.439.50.3729020.9640.1250.3930.88999.9
2.43-2.519.40.3398810.9640.1150.3590.90999.9
2.51-2.69.30.2848940.9660.0970.31.17899.9
2.6-2.79.20.2378780.9760.0810.2511.296100
2.7-2.828.40.2099030.9780.0730.2221.62799.8
2.82-2.979.40.1899140.9830.0630.21.96799.9
2.97-3.169.60.1688990.980.0560.1772.46199.9
3.16-3.49.40.1479080.9850.050.1563.17199.9
3.4-3.748.70.1299170.9890.0450.1373.94599.6
3.74-4.299.60.1169210.9930.0380.1224.54899.9
4.29-5.490.1039350.9930.0350.1095.30199.5
5.4-508.70.11910150.9880.0430.1278.8499.8

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3RRQ & 3BP5

3rrq

3bp5


Resolution: 1.986→37.508 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2262 1774 10 %
Rwork0.1984 --
obs0.2012 17743 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.69 Å2 / Biso mean: 50.7646 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.986→37.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 1 125 1724
Biso mean--10.21 53.67 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141687
X-RAY DIFFRACTIONf_angle_d1.912298
X-RAY DIFFRACTIONf_chiral_restr0.111265
X-RAY DIFFRACTIONf_plane_restr0.011297
X-RAY DIFFRACTIONf_dihedral_angle_d12.8613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.986-2.03950.34481210.2965109090
2.0395-2.09960.30181290.2655115995
2.0996-2.16730.3291330.2527120098
2.1673-2.24480.25881360.23411224100
2.2448-2.33460.26381360.226122199
2.3346-2.44090.26661370.20751234100
2.4409-2.56950.2561360.22091230100
2.5695-2.73050.26821380.21361243100
2.7305-2.94120.2391390.22371244100
2.9412-3.23710.24771380.2031238100
3.2371-3.70510.21421390.18921261100
3.7051-4.66660.18551430.15281282100
4.6666-37.5080.19281490.1928134399

+
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