[English] 日本語
Yorodumi
- PDB-3rnk: Crystal structure of the complex between mouse PD-1 mutant and PD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rnk
TitleCrystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain
Components
  • Programmed cell death 1 ligand 2
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / PD-L2 / B7-DC / Programmed death-1 Ligand 2 / complex / costimulatory / IgV
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T 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 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T 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 / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / cellular response to lipopolysaccharide / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane
Similarity search - Function
Programmed cell death protein 1 / 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 ...Programmed cell death protein 1 / 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 protein 1 / Programmed cell death 1 ligand 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLazar-Molnar, E. / Ramagopal, U.A. / Cao, E. / Nathenson, S.G. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain
Authors: Lazar-Molnar, E. / Ramagopal, U.A. / Cao, E. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2013Group: Other
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9102
Polymers24,9102
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-6 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.057, 60.246, 80.087
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 / Protein PD-1 / mPD-1


Mass: 13218.794 Da / Num. of mol.: 1 / Fragment: Residues 34-150 / Mutation: C83S, A132L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pd1, Pdcd1 / Plasmid: PET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q02242
#2: Protein Programmed cell death 1 ligand 2 / PD-1 ligand 2 / PD-L2 / PDCD1 ligand 2 / Programmed death ligand 2 / Butyrophilin B7-DC / B7-DC


Mass: 11691.254 Da / Num. of mol.: 1 / Fragment: Rsidues 20-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B7dc, Btdc, Cd273, Murine, Pdcd1lg2, Pdl2 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9WUL5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.75 Å3/Da / Density % sol: 29.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7, 0.1M Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 17532 / Num. obs: 17532 / % possible obs: 95.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.62 / Rsym value: 0.63 / Net I/σ(I): 26.23
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4.42 / Rsym value: 0.16 / % possible all: 69.6

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPU,3BOV

1npu

3bov


Resolution: 1.74→48.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2493 / WRfactor Rwork: 0.2006 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8276 / SU B: 2.861 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1555 / SU Rfree: 0.1477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 909 5.2 %RANDOM
Rwork0.1947 ---
obs0.1974 17485 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.45 Å2 / Biso mean: 25.5806 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20 Å2
2--3.2 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.74→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 110 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221747
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9572378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64724.44481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87615296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0141511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211319
X-RAY DIFFRACTIONr_mcbond_it0.9711.51083
X-RAY DIFFRACTIONr_mcangle_it1.81221753
X-RAY DIFFRACTIONr_scbond_it2.3173664
X-RAY DIFFRACTIONr_scangle_it3.8784.5623
LS refinement shellResolution: 1.741→1.786 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 37 -
Rwork0.235 759 -
all-796 -
obs--59.98 %

+
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