[English] 日本語
Yorodumi
- PDB-5jxe: Human PD-1 ectodomain complexed with Pembrolizumab Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jxe
TitleHuman PD-1 ectodomain complexed with Pembrolizumab Fab
Components
  • Pembrolizumab Fab heavy chain
  • Pembrolizumab Fab light chain
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / human PD-1 Pembrolizumab Fab
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS / adaptive immune response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / 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 / Immunoglobulins ...Programmed cell death protein 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNa, Z. / Bharath, S.R. / Song, H.
CitationJournal: Cell Res. / Year: 2017
Title: Structural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab.
Authors: Na, Z. / Yeo, S.P. / Bharath, S.R. / Bowler, M.W. / Balijkcij, E. / Wang, C.I. / Song, H.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Experimental preparation
Revision 1.2Dec 6, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 1
B: Programmed cell death protein 1
C: Pembrolizumab Fab light chain
D: Pembrolizumab Fab heavy chain
F: Pembrolizumab Fab light chain
G: Pembrolizumab Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)120,3286
Polymers120,3286
Non-polymers00
Water18010
1
A: Programmed cell death protein 1
F: Pembrolizumab Fab light chain
G: Pembrolizumab Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)60,1643
Polymers60,1643
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Programmed cell death protein 1
C: Pembrolizumab Fab light chain
D: Pembrolizumab Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)60,1643
Polymers60,1643
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.554, 105.554, 380.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

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


Mass: 12714.137 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 34-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#2: Antibody Pembrolizumab Fab light chain


Mass: 23768.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Pembrolizumab Fab heavy chain


Mass: 23681.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6, 19 mM n-Decyl-N,N-dimethylglycine, 20% isopropanol and 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2016 / Details: Si with Pt coating
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.9→29.926 Å / Num. obs: 28657 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 67.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK, 5DK3

4zqk

5dk3


Resolution: 2.9→29.926 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.97
RfactorNum. reflection% reflection
Rfree0.2857 1424 4.97 %
Rwork0.2606 --
obs0.2619 28637 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 0 10 7851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058032
X-RAY DIFFRACTIONf_angle_d0.79610951
X-RAY DIFFRACTIONf_dihedral_angle_d14.7984769
X-RAY DIFFRACTIONf_chiral_restr0.0461248
X-RAY DIFFRACTIONf_plane_restr0.0071403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.00370.39291310.34582674X-RAY DIFFRACTION100
3.0037-3.12380.34851370.33832594X-RAY DIFFRACTION98
3.1238-3.26580.36711160.33142689X-RAY DIFFRACTION100
3.2658-3.43780.38881410.31712672X-RAY DIFFRACTION100
3.4378-3.65280.33511430.28762709X-RAY DIFFRACTION100
3.6528-3.93430.31611390.27512705X-RAY DIFFRACTION100
3.9343-4.32910.24051680.23982700X-RAY DIFFRACTION100
4.3291-4.95310.23211640.21162740X-RAY DIFFRACTION100
4.9531-6.23120.24661420.23552755X-RAY DIFFRACTION98
6.2312-29.92710.27791430.24342975X-RAY DIFFRACTION98

+
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