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- PDB-7tps: Crystal structure of ALPN-202 (engineered CD80 vIgD) in complex w... -

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Basic information

Entry
Database: PDB / ID: 7tps
TitleCrystal structure of ALPN-202 (engineered CD80 vIgD) in complex with PD-L1
Components
  • (Programmed cell death 1 ligand ...) x 2
  • T-lymphocyte activation antigen CD80
KeywordsIMMUNE SYSTEM / co-stimulatory / Ig-Like / V-type / T-cell / proliferation
Function / homology
Function and homology information


negative regulation of T cell mediated immunity / positive regulation of T-helper 1 cell differentiation / protein complex involved in cell adhesion / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / positive regulation of signal transduction / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / CD28 co-stimulation ...negative regulation of T cell mediated immunity / positive regulation of T-helper 1 cell differentiation / protein complex involved in cell adhesion / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / positive regulation of signal transduction / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / CD28 co-stimulation / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / CTLA4 inhibitory signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / Interleukin-10 signaling / CD28 dependent PI3K/Akt signaling / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / response to cytokine / T cell activation / Constitutive Signaling by Aberrant PI3K in Cancer / recycling endosome membrane / positive regulation of peptidyl-tyrosine phosphorylation / actin cytoskeleton / PIP3 activates AKT signaling / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / receptor ligand activity / intracellular signal transduction / positive regulation of cell migration / immune response / external side of plasma membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
CD80, IgC-like domain / CD80, immunoglobulin variable domain / : / 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. ...CD80, IgC-like domain / CD80, immunoglobulin variable domain / : / 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
T-lymphocyte activation antigen CD80 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsDemonte, D.W. / Maurer, M.F. / Akutsu, M. / Kimbung, Y.R. / Logan, D.T. / Walse, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: The engineered CD80 variant fusion therapeutic davoceticept combines checkpoint antagonism with conditional CD28 costimulation for anti-tumor immunity.
Authors: Maurer, M.F. / Lewis, K.E. / Kuijper, J.L. / Ardourel, D. / Gudgeon, C.J. / Chandrasekaran, S. / Mudri, S.L. / Kleist, K.N. / Navas, C. / Wolfson, M.F. / Rixon, M.W. / Swanson, R. / Dillon, ...Authors: Maurer, M.F. / Lewis, K.E. / Kuijper, J.L. / Ardourel, D. / Gudgeon, C.J. / Chandrasekaran, S. / Mudri, S.L. / Kleist, K.N. / Navas, C. / Wolfson, M.F. / Rixon, M.W. / Swanson, R. / Dillon, S.R. / Levin, S.D. / Kimbung, Y.R. / Akutsu, M. / Logan, D.T. / Walse, B. / Swiderek, K.M. / Peng, S.L.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-lymphocyte activation antigen CD80
B: Programmed cell death 1 ligand 1
C: T-lymphocyte activation antigen CD80
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,20815
Polymers72,5074
Non-polymers3,70211
Water95553
1
A: T-lymphocyte activation antigen CD80
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0987
Polymers36,2932
Non-polymers1,8055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-lymphocyte activation antigen CD80
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1108
Polymers36,2132
Non-polymers1,8976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.928, 122.152, 152.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein T-lymphocyte activation antigen CD80 / Activation B7-1 antigen / BB1 / CTLA-4 counter-receptor B7.1 / B7


Mass: 12245.182 Da / Num. of mol.: 2 / Mutation: H52Y, A60E, E69D, M81L, V102M, A105G, D124G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD80, CD28LG, CD28LG1, LAB7 / Production host: Homo sapiens (human) / References: UniProt: P33681

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Programmed cell death 1 ligand ... , 2 types, 2 molecules BD

#2: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 24048.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7
#3: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 23968.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7

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Sugars , 3 types, 10 molecules

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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Non-polymers , 2 types, 54 molecules

#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 0.1 M sodium HEPES/MOPS (acid), pH 7.5, 20% v/v glycerol, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.15→95.38 Å / Num. obs: 19918 / % possible obs: 99.3 % / Redundancy: 5.4 % / CC1/2: 0.996 / Net I/σ(I): 0.9
Reflection shellResolution: 3.15→3.37 Å / Rmerge(I) obs: 1.722 / Num. unique obs: 107751

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (11-DEC-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DR9, 5JDR

1dr9

5jdr


Resolution: 3.15→76.34 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.469
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 991 4.99 %RANDOM
Rwork0.2474 ---
obs0.2496 19859 99 %-
Displacement parametersBiso max: 193.15 Å2 / Biso mean: 110.9 Å2 / Biso min: 34.14 Å2
Baniso -1Baniso -2Baniso -3
1-16.2071 Å20 Å20 Å2
2---31.8755 Å20 Å2
3---15.6684 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 3.15→76.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 242 53 5316
Biso mean--133.57 60.29 -
Num. residues----621
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1973SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes884HARMONIC5
X-RAY DIFFRACTIONt_it5373HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion781SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3760SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5373HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7310HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion19.44
LS refinement shellResolution: 3.15→3.17 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3005 20 4.93 %
Rwork0.3841 386 -
all0.3799 406 -
obs--94.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.17882.5776-2.25277.0713-2.664.4895-0.0218-0.0840.28780.1323-0.06670.38890.0055-0.21020.0885-0.36370.0202-0.0743-0.0016-0.1024-0.0193-88.3143-18.45641.2277
26.62.41524.31782.27841.9624.9047-0.05520.30810.0642-0.0570.1003-0.191-0.1870.424-0.0451-0.22510.02680.0601-0.14530.01780.0027-51.6804-2.57492.2465
33.4625-1.59170.806515.3529-2.15196.060.2304-0.38090.2758-2.5114-0.39871.2255-1.1425-0.47720.16840.22590.5685-0.467-0.3402-0.1388-0.3591-84.439219.6248-33.4857
45.6585-2.7528-4.77771.21642.65835.73070.02280.0410.17210.17930.0311-0.1527-0.2406-0.0942-0.0539-0.1034-0.041-0.0473-0.10140.1452-0.0792-52.3954-1.6823-36.0527
50.31111.9181-3.300502.273900.2051-0.33060.1655-1.14450.5318-1.3038-0.4662-0.2268-0.7369-0.403-0.1944-0.36450.3808-0.16070.2917-63.8002-0.6472-16.0747
60-0.6351-0.416800.0280-0.1596-0.08940.071-0.01740.0982-0.0752-0.02150.02130.06130.37830.0025-0.1043-0.1966-0.02960.4625-63.9813-7.2605-5.2296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - A|140 A|201 - A|201 }A35 - 140
2X-RAY DIFFRACTION1{ A|35 - A|140 A|201 - A|201 }A201
3X-RAY DIFFRACTION2{ B|19 - B|227 B|301 - B|302 }B19 - 227
4X-RAY DIFFRACTION2{ B|19 - B|227 B|301 - B|302 }B301 - 302
5X-RAY DIFFRACTION3{ C|36 - C|140 C|201 - C|201 }C36 - 140
6X-RAY DIFFRACTION3{ C|36 - C|140 C|201 - C|201 }C201
7X-RAY DIFFRACTION4{ D|19 - D|227 D|301 - D|302 }D19 - 227
8X-RAY DIFFRACTION4{ D|19 - D|227 D|301 - D|302 }D301 - 302
9X-RAY DIFFRACTION5{ D|303 - D|303 }D303
10X-RAY DIFFRACTION6{ A|301 - A|310 B|401 - B|430 C|301 - C|302 }A301 - 310
11X-RAY DIFFRACTION6{ A|301 - A|310 B|401 - B|430 C|301 - C|302 }B401 - 430
12X-RAY DIFFRACTION6{ A|301 - A|310 B|401 - B|430 C|301 - C|302 }C301 - 302

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