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- PDB-7ygg: Crystal structure of human CD47 in complex with engineered SIRPa.... -

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Basic information

Entry
Database: PDB / ID: 7ygg
TitleCrystal structure of human CD47 in complex with engineered SIRPa.D1(N80A)
Components
  • Leukocyte surface antigen CD47
  • SIRPA protein
KeywordsIMMUNE SYSTEM / SIRPa-Fc fusion protein / IMM01
Function / homology
Function and homology information


cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / cell-cell adhesion mediator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of type II interferon production / ATP export / fibrinogen binding ...cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / cell-cell adhesion mediator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of type II interferon production / ATP export / fibrinogen binding / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of phagocytosis / thrombospondin receptor activity / tertiary granule membrane / cellular response to interleukin-1 / Integrin cell surface interactions / specific granule membrane / positive regulation of stress fiber assembly / positive regulation of phagocytosis / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cellular response to type II interferon / positive regulation of inflammatory response / cell migration / angiogenesis / inflammatory response / positive regulation of cell population proliferation / apoptotic process / Neutrophil degranulation / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsYu, J. / Tian, W.
Funding support1items
OrganizationGrant numberCountry
Immuneonco Biopharmaceuticals (Shanghai) Inc.
CitationJournal: Molecules / Year: 2022
Title: Crystal Structure of Human CD47 in Complex with Engineered SIRP alpha.D1(N80A).
Authors: Yu, J. / Li, S. / Chen, D. / Liu, D. / Guo, H. / Yang, C. / Zhang, W. / Zhang, L. / Zhao, G. / Tu, X. / Peng, L. / Liu, S. / Bai, X. / Song, Y. / Jiang, Z. / Zhang, R. / Tian, W.
History
DepositionJul 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIRPA protein
B: SIRPA protein
C: Leukocyte surface antigen CD47
D: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,08311
Polymers59,0124
Non-polymers1,0717
Water2,594144
1
A: SIRPA protein
C: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0736
Polymers29,5062
Non-polymers5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint8 kcal/mol
Surface area12110 Å2
MethodPISA
2
B: SIRPA protein
D: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0115
Polymers29,5062
Non-polymers5043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint7 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.580, 99.640, 138.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SIRPA protein


Mass: 15261.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence has been deposited to Genbank with accession number AAH26692.1. Residue N80A represents mutation.
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRPA / Plasmid: pTT5-SP-CD47-His / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#2: Protein Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 14245.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Plasmid: pTT5-SP-CD47-His / Production host: Homo sapiens (human) / Strain (production host): Expi293F / References: UniProt: Q08722
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 4 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.76→47.19 Å / Num. obs: 19839 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.977 / Rmerge(I) obs: 0.288 / Rpim(I) all: 0.109 / Rrim(I) all: 0.309 / Net I/σ(I): 10.1 / Num. measured all: 168759
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.76-2.918.21.4192308228100.5170.5421.5232.699.9
8.73-47.197.90.06956917200.9970.0270.07424.599.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDS1.10.2022data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZ2, 2JJS

5tz2

2jjs


Resolution: 2.76→47.19 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 26.921 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.642 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 964 4.9 %RANDOM
Rwork0.2173 ---
obs0.2196 18821 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.96 Å2 / Biso mean: 49.453 Å2 / Biso min: 19.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å2-0 Å2-0 Å2
2---1.69 Å20 Å2
3---3.66 Å2
Refinement stepCycle: final / Resolution: 2.76→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 68 144 3823
Biso mean--61.32 37.67 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133771
X-RAY DIFFRACTIONr_bond_other_d0.0030.0153545
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.6775112
X-RAY DIFFRACTIONr_angle_other_deg1.0741.5978227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1895467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90422.874174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63415648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0751518
X-RAY DIFFRACTIONr_chiral_restr0.0340.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
LS refinement shellResolution: 2.76→2.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 66 -
Rwork0.346 1361 -
all-1427 -
obs--99.79 %
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)
11.63442.859-3.90427.0912-7.03310.1841-0.0183-0.2381-0.26210.0671-0.2833-0.2181-0.09230.51440.30150.03650.02120.03810.17940.01690.22844.20713.279.692
20.3240.3720.24712.0297-0.64510.7541-0.1259-0.06740.0631-0.0278-0.0231-0.0151-0.1596-0.02140.1490.06190.0181-0.00690.27250.01030.183736.47616.9390.3
31.40662.18771.02625.6649-0.72943.5311-0.11650.1433-0.0666-0.41420.0731-0.09240.306-0.02970.04340.0912-0.09780.05570.2785-0.040.140732.3267.733-2.008
42.0036-0.0045-1.36132.1869-0.76411.2115-0.1094-0.0463-0.00620.06620.1184-0.09720.0685-0.0186-0.0090.0342-0.0454-0.03940.2277-0.03580.146234.18518.7062.773
52.74010.9315-2.78564.5579-4.817913.4907-0.0661-0.1353-0.1135-0.204-0.2296-0.2705-0.2840.46560.29560.05660.0192-0.00770.13010.01520.099545.75324.525-12.904
62.6035-0.44354.63030.19720.399720.5195-0.16330.32120.140.0063-0.0845-0.0195-0.55450.47530.24770.1798-0.0491-0.08680.10620.0060.11320.89139.10535.454
70.75720.71411.78171.86241.99275.2199-0.09720.05120.22450.1548-0.337-0.21010.1217-0.1430.43420.1524-0.1176-0.12850.20310.09320.281120.54930.43344.806
83.36810.94124.68561.75530.742210.15930.4539-0.6346-0.45850.3004-0.3654-0.19680.5373-0.5887-0.08850.2181-0.1329-0.03280.19640.10730.164113.51723.0948.991
92.8695-0.4394-2.94342.01440.55593.06870.59750.31090.42180.5167-0.15820.2692-0.6294-0.3666-0.43930.44330.17480.11280.2118-0.07440.25637.34733.82440.658
102.6861-0.02182.44383.25591.14786.5508-0.26890.1050.4530.0565-0.0673-0.0829-0.61320.10110.33620.1050.0122-0.09020.0245-0.01450.139222.43629.29447.931
110.7810.91062.19051.25732.93196.89110.05830.16510.02660.19680.0582-0.05550.3970.1946-0.11650.1168-0.0369-0.07220.2065-0.02740.232324.12829.97944.27
1215.88433.15796.08191.71581.74782.84490.31740.90250.4119-0.0717-0.2722-0.27290.26380.2019-0.04510.23150.09150.07430.33730.09570.189518.771.619-2.763
136.90240.91572.07720.15450.09789.27740.186-0.1182-0.11620.0233-0.03110.06980.1352-0.0105-0.1550.0522-0.0250.00850.068-0.05990.2436-0.4651.3113.728
142.13310.4103-0.27140.92470.14570.0924-0.1335-0.0503-1.35470.139-0.0553-0.10810.0604-0.01050.18880.0451-0.02740.10250.21440.04510.909522.252-3.0666.162
151.2955-0.3227-0.40433.02410.24740.1611-0.23320.12050.03940.47160.1799-0.01680.08130.00090.05320.1094-0.007-0.04030.31070.03860.162314.7549.38313.366
163.1104-4.62640.69378.0024-0.44630.4617-0.1175-0.199-0.16650.62840.13550.26790.2124-0.1347-0.0180.1974-0.04120.04520.15860.03260.118113.667-1.70912.509
176.0895-4.10143.2274.9801-0.27398.7246-0.0987-0.3182-0.04980.1684-0.01040.07440.265-0.67190.10920.0367-0.04710.03370.13220.00040.0950.7396.219.159
189.9202-2.36831.17990.5798-0.24960.2212-0.03510.0579-0.07360.0285-0.0460.0450.0412-0.03480.08120.0333-0.02160.02920.2563-0.01770.164811.7336.2111.856
191.2738-1.1312-0.189.8883-6.07134.4039-0.1914-0.14410.38351.5040.3599-0.1774-0.8789-0.1667-0.16850.35680.0063-0.03870.2296-0.06520.12621.85216.36742.99
200.8877-0.6403-0.44264.66311.35290.5201-0.1314-0.26510.1940.11630.09510.35540.10190.0120.03630.06620.0010.00710.3291-0.05370.13932.03311.30232.854
210.8215-0.70222.60457.7361-5.5949.85370.0142-0.0009-0.0112-0.02-0.0609-0.11750.060.01570.04670.04760.05220.04160.19370.01380.116611.8212.17326.379
225.0415-4.75230.05856.06031.62362.05930.00840.1076-0.18170.0994-0.26490.29680.2277-0.29260.25650.0551-0.05280.06430.2340.01680.12143.10111.0826.553
230.44541.56220.36037.2570.42071.4380.0273-0.13720.02040.2565-0.05790.32130.0985-0.29030.03060.0913-0.00220.0610.19030.02970.08356.0437.00832.712
241.01061.35190.34719.8355-2.01520.88850.3452-0.34710.11080.8085-0.28360.44180.009-0.1839-0.06160.164-0.08420.08680.24140.03160.07933.0214.56240.06
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 50
3X-RAY DIFFRACTION3A51 - 75
4X-RAY DIFFRACTION4A76 - 108
5X-RAY DIFFRACTION5A109 - 117
6X-RAY DIFFRACTION6B1 - 11
7X-RAY DIFFRACTION7B12 - 50
8X-RAY DIFFRACTION8B51 - 62
9X-RAY DIFFRACTION9B63 - 75
10X-RAY DIFFRACTION10B76 - 95
11X-RAY DIFFRACTION11B96 - 116
12X-RAY DIFFRACTION12C1 - 8
13X-RAY DIFFRACTION13C9 - 21
14X-RAY DIFFRACTION14C22 - 32
15X-RAY DIFFRACTION15C33 - 63
16X-RAY DIFFRACTION16C64 - 79
17X-RAY DIFFRACTION17C80 - 90
18X-RAY DIFFRACTION18C91 - 116
19X-RAY DIFFRACTION19D1 - 8
20X-RAY DIFFRACTION20D9 - 42
21X-RAY DIFFRACTION21D43 - 58
22X-RAY DIFFRACTION22D59 - 79
23X-RAY DIFFRACTION23D80 - 102
24X-RAY DIFFRACTION24D103 - 116

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