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- PDB-5jxe: Human PD-1 ectodomain complexed with Pembrolizumab Fab -

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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 / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...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 / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / 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 / Immunoglobulin-like fold ...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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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