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- PDB-4kjy: Complex of high-affinity SIRP alpha variant FD6 with CD47 -

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Basic information

Entry
Database: PDB / ID: 4kjy
TitleComplex of high-affinity SIRP alpha variant FD6 with CD47
Components
  • High-affinity SIRPa variant FD6
  • Leukocyte surface antigen CD47
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Immune regulation / N-linked glycosylation / Plasma membrane
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 / regulation of type II interferon production / ATP export / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / cell-cell adhesion mediator activity / regulation of tumor necrosis factor production ...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 / regulation of type II interferon production / ATP export / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / cell-cell adhesion mediator activity / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / cellular response to interleukin-1 / Integrin cell surface interactions / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cellular response to type II interferon / positive regulation of inflammatory response / cell migration / positive regulation of T cell activation / angiogenesis / inflammatory response / apoptotic process / positive regulation of cell population proliferation / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsRing, A.M. / Ozkan, E. / Ho, C.C.M. / Garcia, K.C.
CitationJournal: Science / Year: 2013
Title: Engineered SIRP alpha variants as immunotherapeutic adjuvants to anticancer antibodies.
Authors: Weiskopf, K. / Ring, A.M. / Ho, C.C. / Volkmer, J.P. / Levin, A.M. / Volkmer, A.K. / Ozkan, E. / Fernhoff, N.B. / van de Rijn, M. / Weissman, I.L. / Garcia, K.C.
History
DepositionMay 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte surface antigen CD47
B: High-affinity SIRPa variant FD6
C: Leukocyte surface antigen CD47
D: High-affinity SIRPa variant FD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,59415
Polymers57,5374
Non-polymers2,05811
Water6,810378
1
A: Leukocyte surface antigen CD47
B: High-affinity SIRPa variant FD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5286
Polymers28,7682
Non-polymers7604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-8 kcal/mol
Surface area11410 Å2
MethodPISA
2
C: Leukocyte surface antigen CD47
D: High-affinity SIRPa variant FD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0669
Polymers28,7682
Non-polymers1,2987
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-12 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.340, 71.340, 399.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-300-

HOH

21C-308-

HOH

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Components

#1: Antibody Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 14245.014 Da / Num. of mol.: 2 / Mutation: C15G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Plasmid: pAcGP67a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08722
#2: Antibody High-affinity SIRPa variant FD6


Mass: 14523.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMal-p2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS RESIDUE IS ENCODED AS GLUTAMINE, BUT SPONTANEOUSLY CYCLIZES TO PYROGLUTAMIC ACID.

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Crystals were obtained by addition of 0.1 microL protein to an equal volume of 2.0 M ammonium sulfate and 0.1 M Tris, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 36706 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 21.4
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.93130.3
1.93-1.97139.4
1.97-2.01145.2
2.01-2.05151.8
2.05-2.09160.7
2.09-2.14164.7
2.14-2.19175.3
2.19-2.25190
2.25-2.32198.8
2.32-2.391100
2.39-2.481100
2.48-2.581100
2.58-2.71100
2.7-2.841100
2.84-3.021100
3.02-3.251100
3.25-3.581100
3.58-4.091100
4.09-5.16199.2
5.16-50197.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→31.291 Å / SU ML: 0.25 / σ(F): 1.32 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 1476 4.02 %
Rwork0.2189 --
obs0.2206 36706 78.03 %
all-49097 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→31.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 127 378 4006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063719
X-RAY DIFFRACTIONf_angle_d0.9475057
X-RAY DIFFRACTIONf_dihedral_angle_d12.4861336
X-RAY DIFFRACTIONf_chiral_restr0.059601
X-RAY DIFFRACTIONf_plane_restr0.004636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.98950.407790.3467319X-RAY DIFFRACTION8
1.9895-2.06060.291430.2619927X-RAY DIFFRACTION23
2.0606-2.14310.3448680.2621783X-RAY DIFFRACTION44
2.1431-2.24060.32171240.28393167X-RAY DIFFRACTION78
2.2406-2.35870.30561710.26153978X-RAY DIFFRACTION99
2.3587-2.50640.31951700.26824026X-RAY DIFFRACTION100
2.5064-2.69980.30291740.2624080X-RAY DIFFRACTION100
2.6998-2.97130.30321720.25044112X-RAY DIFFRACTION100
2.9713-3.40080.24021770.20724143X-RAY DIFFRACTION100
3.4008-4.28290.23521780.17874204X-RAY DIFFRACTION100
4.2829-31.29470.22371900.18794491X-RAY DIFFRACTION99
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)
10.8855-0.5389-0.6765.3073-1.14244.3854-0.34030.72370.5788-0.90090.2774-1.4542-0.52341.51720.06630.8924-0.51420.16031.1132-0.21170.813310.157227.2118-36.352
22.695-0.8988-0.25343.1872-0.97655.2243-0.25820.5361-0.0308-0.60710.1466-0.37430.13930.95360.10770.5409-0.06270.04560.5911-0.19690.32741.591116.5042-30.8862
32.0001-2.0662-6.38278.0513-0.20884.9975-0.4409-0.5373-0.5845-0.07970.2535-0.34120.60031.33690.19140.64170.1780.10180.7157-0.29790.52464.77666.2863-27.2751
45.0474-1.2532-1.17716.0659-1.15861.5452-0.0373-0.11060.2495-0.52360.1534-0.90890.19921.4109-0.12610.5483-0.03630.14740.9618-0.29820.58319.566815.9286-30.6208
52.0001-0.1719-6.85352.0209-1.80327.5874-0.5793-0.761-0.3496-1.0120.0318-1.01390.74981.21360.5491.071-0.26130.39711.5607-0.36360.958216.006718.1325-41.4106
67.1157-0.0494-6.49484.48012.09888.8195-0.0350.68330.3703-0.89370.5114-0.574-0.8450.4909-0.49570.6033-0.15930.07260.4839-0.19940.286-1.274118.4228-34.1025
74.01251.43540.81842.40140.06910.1944-0.29680.7030.2497-0.76270.2812-0.6041-0.46880.6793-0.01180.7887-0.38540.11580.6405-0.17170.41723.034424.3584-39.1927
87.25920.94380.88146.24460.09132.59750.17440.0441-0.8075-0.1330.17560.89530.3979-0.7904-0.36940.4665-0.28740.11210.5425-0.17820.2871-27.252614.0639-34.4543
92.1562-0.60860.93492.41571.43653.70380.04540.2922-0.0279-0.1539-0.03040.0234-0.0178-0.0902-0.0160.45-0.15910.0890.1957-0.08760.1598-16.445315.6405-37.5029
109.14760.09445.25694.5172-0.0827.207-0.16130.26870.3217-0.01490.20960.0124-0.4017-0.2013-0.02710.39-0.00940.07450.2728-0.12920.1978-21.312421.5323-34.5484
116.99521.46793.43976.49722.67996.9970.4296-0.1851-0.5783-0.087-0.05210.33490.5483-0.3196-0.36860.5093-0.34790.06120.2422-0.23210.1763-18.56059.5314-37.6006
125.4311-1.8469-1.31186.35710.82130.68910.08371.0305-0.7348-0.4097-0.01160.45430.3471-0.209-0.0060.6942-0.29510.07260.4758-0.21170.1427-19.49459.4156-38.834
131.99981.735-6.29514.44831.8675.2920.15830.20580.7289-0.61430.0922-0.404-0.4830.1508-0.2750.583-0.177-0.04690.2136-0.0760.412814.620324.469-2.1356
148.28955.0526-4.9864.9562-0.25297.1342-0.85330.003-1.9851-0.89590.2453-2.4890.80661.04680.62850.7277-0.18490.29710.5499-0.05321.315827.871511.8294-6.5919
151.61620.6586-0.1663.05590.84511.1606-0.0254-0.13520.10730.10020.0816-0.2118-0.22590.1806-0.07840.4738-0.0503-0.10950.0835-0.07580.32099.609615.82153.9896
163.2996-0.3851-0.0648.2558-0.19553.463-0.20210.0871-0.0936-0.18680.1213-0.62570.29960.27840.07590.3243-0.030.03650.1224-0.04610.390111.70224.8771-1.8302
172.69031.1266-0.60155.29080.82144.4845-0.2610.2399-0.4034-0.50490.1695-1.12360.23820.50050.03990.4433-0.09640.03720.1399-0.06380.566316.733311.7948-1.9789
185.54411.8395-2.7544.6582-0.53373.7317-0.50270.3977-0.1243-0.79260.2301-0.68890.16950.13520.20320.5756-0.1687-0.06810.1344-0.10080.324113.195618.0203-5.3133
198.506-5.83675.75282.0023-5.99198.6817-0.6123-1.2470.04191.36580.82110.186-1.1203-1.5494-0.20510.58930.09610.01060.5695-0.08190.2444-16.506920.20484.527
200.4895-0.68430.43211.0089-0.89971.9506-0.0152-00.07780.1235-0.07040.0935-0.2274-0.12640.08320.52980.1544-0.08380.2607-0.13860.3331-16.45635.1159-9.5477
210.3973-0.12770.23290.5132-0.33671.6325-0.0336-0.1344-0.02750.1548-0.06590.1113-0.1279-0.15550.06190.42650.1188-0.0926-0.0254-0.34680.1073-8.710719.6364-3.1664
223.9177-5.4811.96072.0029-4.36184.30060.23870.24940.6283-1.2904-0.1932-1.18520.16590.3073-0.04830.53790.0147-0.09570.1724-0.07940.5309-1.021127.0391-7.729
234.0487-3.41621.26044.7782-3.30983.0569-0.1689-0.28260.39150.60190.0967-0.3707-0.65090.13580.05490.62070.0946-0.27260.1965-0.29680.2826-3.635528.02896.1613
244.74880.86466.7422.33012.55042.0001-0.28060.12660.5162-0.4525-0.0222-0.1272-0.93730.11830.30910.54190.0869-0.13130.1651-0.09290.3409-11.588932.4724-13.6367
254.5567-0.41281.69942.03921.7956.18270.1359-0.1743-0.3070.08270.0690.20560.2826-0.0508-0.22430.33320.0697-0.09580.0995-0.24470.1621-11.294618.0067-4.3107
262.7024-1.1631-0.03242.0446-0.28170.5754-0.02780.1907-0.4651-0.0683-0.03650.13950.0796-0.12130.09830.3448-0.0012-0.03970.1197-0.06860.2933-7.747611.6152-2.0106
274.4306-5.43652.84242.0014-5.79238.68960.4320.24680.0552-1.1907-0.09041.00860.3977-0.0972-0.31670.46880.1771-0.02050.2265-0.1050.2967-20.280734.2095-13.8485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2: 21 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 22: 51 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 52: 58 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 59: 79 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 80: 92 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 93:102 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 103:114 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 1: 23 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 24: 62 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 63: 86 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 87: 95 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 96:114 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 2: 8 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 9: 21 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 22: 42 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 43: 69 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 70:100 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 101:114 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 2: 11 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 12: 23 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 24: 50 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 51: 62 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 63: 75 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 76: 86 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 87: 95 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 96:108 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 109:117 )

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