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- PDB-6jjp: Crystal structure of Fab of a PD-1 monoclonal antibody MW11-h317 ... -

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Basic information

Entry
Database: PDB / ID: 6jjp
TitleCrystal structure of Fab of a PD-1 monoclonal antibody MW11-h317 in complex with PD-1
Components
  • Heavy chain of MW11-h317
  • Programmed cell death protein 1
  • light chain of MW11-h317
KeywordsIMMUNE SYSTEM / PD-1 / monoclonal antibody / cancer treatment
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / 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 / B cell apoptotic process / negative regulation of immune response / 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
AuthorsWang, M. / Wang, J. / Wang, R. / Jiao, S. / Wang, S. / Zhang, J. / Zhang, M.
CitationJournal: Commun Biol / Year: 2019
Title: Identification of a monoclonal antibody that targets PD-1 in a manner requiring PD-1 Asn58 glycosylation.
Authors: Wang, M. / Wang, J. / Wang, R. / Jiao, S. / Wang, S. / Zhang, J. / Zhang, M.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of MW11-h317
B: light chain of MW11-h317
C: Programmed cell death protein 1
D: Heavy chain of MW11-h317
E: light chain of MW11-h317
F: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,89512
Polymers126,2216
Non-polymers2,6746
Water1448
1
A: Heavy chain of MW11-h317
B: light chain of MW11-h317
C: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4486
Polymers63,1103
Non-polymers1,3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-2 kcal/mol
Surface area24600 Å2
MethodPISA
2
D: Heavy chain of MW11-h317
E: light chain of MW11-h317
F: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4486
Polymers63,1103
Non-polymers1,3373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint1 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.610, 54.219, 126.082
Angle α, β, γ (deg.)90.000, 113.920, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C
21(chain F and resid 30 through 146)
12chain A
22chain D
13(chain B and resid 1 through 213)
23chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain CC30 - 401
211(chain F and resid 30 through 146)F30 - 146
112chain AA1 - 220
212chain DD1 - 220
113(chain B and resid 1 through 213)B1 - 213
213chain EE1 - 213

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Heavy chain of MW11-h317


Mass: 23004.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody light chain of MW11-h317


Mass: 23647.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Non-polymers , 2 types, 10 molecules CF

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


Mass: 16458.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q15116
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 6 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris (pH 6.5) and 28% polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 28800 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 57.34 Å2 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.092 / Rrim(I) all: 0.172 / Χ2: 1.01 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.9-34.20.98628740.5490.5551.028100
3-3.124.20.7428590.6590.4171.0371000.851
3.12-3.274.20.48628300.8110.2731.0381000.559
3.27-3.444.20.34228670.8960.1920.9921000.393
3.44-3.654.10.24228340.940.1371.0271000.279
3.65-3.944.10.19528780.9580.111.02499.80.225
3.94-4.334.10.12228570.9840.0690.9741000.14
4.33-4.964.10.09529040.9890.0531.00399.90.109
4.96-6.2440.10329130.9880.0590.9871000.119
6.24-503.90.0629840.9950.0350.99199.60.07

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ, 5WT9

3rrq

5wt9


Resolution: 2.9→40.685 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.91
RfactorNum. reflection% reflection
Rfree0.2473 1464 5.09 %
Rwork0.2068 --
obs0.209 28784 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.06 Å2 / Biso mean: 55.2541 Å2 / Biso min: 29.4 Å2
Refinement stepCycle: final / Resolution: 2.9→40.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8408 0 176 8 8592
Biso mean--59.99 42.6 -
Num. residues----1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038811
X-RAY DIFFRACTIONf_angle_d0.63912001
X-RAY DIFFRACTIONf_chiral_restr0.0431372
X-RAY DIFFRACTIONf_plane_restr0.0051527
X-RAY DIFFRACTIONf_dihedral_angle_d12.6755292
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1144X-RAY DIFFRACTION5.852TORSIONAL
12F1144X-RAY DIFFRACTION5.852TORSIONAL
21A1990X-RAY DIFFRACTION5.852TORSIONAL
22D1990X-RAY DIFFRACTION5.852TORSIONAL
31B2032X-RAY DIFFRACTION5.852TORSIONAL
32E2032X-RAY DIFFRACTION5.852TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.889-2.99230.35951470.30342589273694
2.9923-3.1120.34011370.299627312868100
3.112-3.25360.31191350.269227102845100
3.2536-3.42510.30311350.246827562891100
3.4251-3.63950.24121530.233227112864100
3.6395-3.92030.27121470.217827322879100
3.9203-4.31450.20961330.178927302863100
4.3145-4.93780.20141660.147927562922100
4.9378-6.21760.20321540.183427562910100
6.2176-40.68910.24811570.189728493006100

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