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- PDB-6j14: Complex structure of GY-14 and PD-1 -

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Basic information

Entry
Database: PDB / ID: 6j14
TitleComplex structure of GY-14 and PD-1
Components
  • GY-14 heavy chain V fragment
  • GY-14 light chain V fragment
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / tumor immunotherapy / complex structure / FG loop
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChen, D. / Tan, S. / Whang, H. / Zhang, H. / Chai, Y. / Qi, J. / Yan, J. / Gao, G.F.
CitationJournal: Iscience / Year: 2019
Title: The FG Loop of PD-1 Serves as a "Hotspot" for Therapeutic Monoclonal Antibodies in Tumor Immune Checkpoint Therapy.
Authors: Chen, D. / Tan, S. / Zhang, H. / Wang, H. / He, W. / Shi, R. / Tong, Z. / Zhu, J. / Cheng, H. / Gao, S. / Chai, Y. / Qi, J. / Xiao, M. / Yan, J. / Gao, G.F.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GY-14 heavy chain V fragment
B: GY-14 light chain V fragment
G: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)38,4593
Polymers38,4593
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-21 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.422, 75.679, 55.873
Angle α, β, γ (deg.)90.00, 104.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody GY-14 heavy chain V fragment


Mass: 13149.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#2: Antibody GY-14 light chain V fragment


Mass: 12421.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#3: Protein Programmed cell death protein 1 / / hPD-1


Mass: 12887.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q15116
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 0.06 M MgCl2, CaCl2, 0.1 M imidazole-MES (pH 6.5), 18% v/v ethylene glycol and polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 66956 / % possible obs: 97.07 % / Redundancy: 7 % / Net I/σ(I): 7.69
Reflection shellResolution: 1.4→1.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ,3EYQ

3rrq

3eyq


Resolution: 1.4→44.032 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.215 3350 5 %
Rwork0.1876 --
obs0.1889 66956 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→44.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 0 392 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072633
X-RAY DIFFRACTIONf_angle_d0.9333577
X-RAY DIFFRACTIONf_dihedral_angle_d18.45963
X-RAY DIFFRACTIONf_chiral_restr0.085391
X-RAY DIFFRACTIONf_plane_restr0.006457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3989-1.41890.23371330.21362513X-RAY DIFFRACTION94
1.4189-1.44010.21200.20042615X-RAY DIFFRACTION95
1.4401-1.46260.22211380.19532592X-RAY DIFFRACTION96
1.4626-1.48660.21021670.19632544X-RAY DIFFRACTION96
1.4866-1.51220.23671470.19242614X-RAY DIFFRACTION95
1.5122-1.53970.24821210.19482652X-RAY DIFFRACTION96
1.5397-1.56930.23271550.19342573X-RAY DIFFRACTION96
1.5693-1.60140.19751650.18492611X-RAY DIFFRACTION96
1.6014-1.63620.21051380.18642612X-RAY DIFFRACTION97
1.6362-1.67420.22231540.192650X-RAY DIFFRACTION97
1.6742-1.71610.23651260.19382641X-RAY DIFFRACTION97
1.7161-1.76250.22191380.19092611X-RAY DIFFRACTION97
1.7625-1.81440.21781420.19092672X-RAY DIFFRACTION97
1.8144-1.87290.22621420.18812640X-RAY DIFFRACTION97
1.8729-1.93990.24131290.19092659X-RAY DIFFRACTION97
1.9399-2.01760.2171500.18352654X-RAY DIFFRACTION98
2.0176-2.10940.2161390.17992672X-RAY DIFFRACTION98
2.1094-2.22060.19581350.18242685X-RAY DIFFRACTION98
2.2206-2.35970.24161430.18832684X-RAY DIFFRACTION98
2.3597-2.54190.21561550.19852713X-RAY DIFFRACTION98
2.5419-2.79760.23051260.19592718X-RAY DIFFRACTION99
2.7976-3.20240.22071260.18952717X-RAY DIFFRACTION99
3.2024-4.03420.17331340.17872762X-RAY DIFFRACTION99
4.0342-44.05390.21661270.18032802X-RAY DIFFRACTION99

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