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- PDB-6sru: Structure of Ig-like V-type domian of mouse Programmed cell death... -

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Basic information

Entry
Database: PDB / ID: 6sru
TitleStructure of Ig-like V-type domian of mouse Programmed cell death 1 ligand 1 (PD-L1)
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / immune checkpoint protein
Function / homology
Function and homology information


PD-1 signaling / positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / : / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...PD-1 signaling / positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / : / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / membrane => GO:0016020 / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / cell surface / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.532 Å
AuthorsMagiera-Mularz, K. / Sala, D. / Grudnik, P. / Holak, T.A.
Funding support Poland, 1items
OrganizationGrant numberCountry
European UnionPOIR.04.04.00-00-420F/17-00 Poland
CitationJournal: Iscience / Year: 2021
Title: Human and mouse PD-L1: similar molecular structure, but different druggability profiles.
Authors: Magiera-Mularz, K. / Kocik, J. / Musielak, B. / Plewka, J. / Sala, D. / Machula, M. / Grudnik, P. / Hajduk, M. / Czepiel, M. / Siedlar, M. / Holak, T.A. / Skalniak, L.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
E: Programmed cell death 1 ligand 1
F: Programmed cell death 1 ligand 1
G: Programmed cell death 1 ligand 1
H: Programmed cell death 1 ligand 1
I: Programmed cell death 1 ligand 1
J: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)133,35210
Polymers133,35210
Non-polymers00
Water70339
1
A: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)13,3351
Polymers13,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.920, 107.715, 79.531
Angle α, β, γ (deg.)90.000, 99.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 13335.218 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd274, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EP73
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris pH 7.5, 20% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978631 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978631 Å / Relative weight: 1
ReflectionResolution: 2.53→49.664 Å / Num. obs: 38622 / % possible obs: 94.1 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.8
Reflection shellResolution: 2.53→2.62 Å / Rmerge(I) obs: 0.826 / Num. unique obs: 3645 / CC1/2: 0.567

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.532→49.664 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.04
RfactorNum. reflection% reflection
Rfree0.2791 1906 4.95 %
Rwork0.2276 --
obs0.2302 38487 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.24 Å2 / Biso mean: 67.5675 Å2 / Biso min: 29.01 Å2
Refinement stepCycle: final / Resolution: 2.532→49.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8635 0 0 41 8676
Biso mean---55.31 -
Num. residues----1146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.532-2.59480.3886121248790
2.5948-2.6650.3881200.3349257291
2.665-2.74340.39121310.3189268897
2.7434-2.83190.34841410.3031270397
2.8319-2.93310.35011490.287267397
2.9331-3.05050.33491630.274266197
3.0505-3.18940.32491400.2825265495
3.1894-3.35750.31991230.2664257593
3.3575-3.56780.30931470.2452265496
3.5678-3.84320.33521290.2565240686
3.8432-4.22970.24781450.1904250991
4.2297-4.84130.20691350.166266095
4.8413-6.09780.20521290.1837267495
6.0978-49.6640.27311330.2177266593
Refinement TLS params.Method: refined / Origin x: -25.5684 Å / Origin y: 9.7072 Å / Origin z: 17.0503 Å
111213212223313233
T0.3165 Å2-0.0104 Å20.0012 Å2-0.3192 Å2-0.0094 Å2--0.3119 Å2
L0.0288 °20.0045 °20.0204 °2-0.0131 °2-0.0071 °2---0.0469 °2
S-0.003 Å °-0.0219 Å °0.0337 Å °0.004 Å °-0.0057 Å °-0.0028 Å °0.0618 Å °-0.0279 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 134
2X-RAY DIFFRACTION1allB19 - 134
3X-RAY DIFFRACTION1allC19 - 133
4X-RAY DIFFRACTION1allD19 - 133
5X-RAY DIFFRACTION1allE19 - 134
6X-RAY DIFFRACTION1allF19 - 134
7X-RAY DIFFRACTION1allG19 - 134
8X-RAY DIFFRACTION1allH19 - 134
9X-RAY DIFFRACTION1allI19 - 133
10X-RAY DIFFRACTION1allJ19 - 134
11X-RAY DIFFRACTION1allK3 - 59

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