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- PDB-7v63: Structure of dimeric uPAR at low pH -

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Basic information

Entry
Database: PDB / ID: 7v63
TitleStructure of dimeric uPAR at low pH
ComponentsUrokinase plasminogen activator surface receptorUrokinase receptor
KeywordsIMMUNE SYSTEM / GPI-anchored protein
Function / homology
Function and homology information


urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / regulation of proteolysis / serine-type endopeptidase complex ...urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / regulation of proteolysis / serine-type endopeptidase complex / Dissolution of Fibrin Clot / positive regulation of epidermal growth factor receptor signaling pathway / extrinsic component of membrane / positive regulation of release of cytochrome c from mitochondria / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / specific granule membrane / regulation of cell adhesion / cell projection / chemotaxis / blood coagulation / signaling receptor activity / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / signal transduction / extracellular region / membrane / plasma membrane
Similarity search - Function
CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / Ly-6 antigen / uPA receptor -like domain / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / Snake toxin-like superfamily
Similarity search - Domain/homology
Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.906 Å
AuthorsYuan, C. / Huang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077016, 82070142, 31570745, 31670739 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structure and cellular functions of uPAR dimer
Authors: Yu, S. / Sui, Y. / Wang, J. / Li, Y. / Li, H. / Cao, Y. / Chen, L. / Jiang, L. / Yuan, C. / Huang, M.
History
DepositionAug 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase plasminogen activator surface receptor
B: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7715
Polymers62,1082
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint3 kcal/mol
Surface area24650 Å2
Unit cell
Length a, b, c (Å)77.449, 77.449, 275.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 79 or resid 154 through 251 or resid 261 through 277 or resid 1172))
21(chain B and (resid 1 through 51 or resid 59...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 79 or resid 154 through 251 or resid 261 through 277 or resid 1172))A1 - 79
121(chain A and (resid 1 through 79 or resid 154 through 251 or resid 261 through 277 or resid 1172))A154 - 251
131(chain A and (resid 1 through 79 or resid 154 through 251 or resid 261 through 277 or resid 1172))A261 - 277
141(chain A and (resid 1 through 79 or resid 154 through 251 or resid 261 through 277 or resid 1172))A1172
211(chain B and (resid 1 through 51 or resid 59...B1 - 51
221(chain B and (resid 1 through 51 or resid 59...B59 - 79
231(chain B and (resid 1 through 51 or resid 59...B154 - 1
241(chain B and (resid 1 through 51 or resid 59...B0 - 277
251(chain B and (resid 1 through 51 or resid 59...B0 - 277
261(chain B and (resid 1 through 51 or resid 59...B0 - 277
271(chain B and (resid 1 through 51 or resid 59...B0 - 277
281(chain B and (resid 1 through 51 or resid 59...B0 - 277
291(chain B and (resid 1 through 51 or resid 59...B0 - 277

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Components

#1: Protein Urokinase plasminogen activator surface receptor / Urokinase receptor / uPAR / Monocyte activation antigen Mo3


Mass: 31053.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPAR / Plasmid: PMT/BIP / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 Cells / References: UniProt: Q03405
#2: 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.: 3 / 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
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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8-2.2 M ammonium sulphate in 50 mM sodium acetate at pH 4.5-5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17605 / % possible obs: 90.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.126 / Χ2: 0.969 / Net I/σ(I): 7.6 / Num. measured all: 157976
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.9-35.30.3139060.672148.2
3-3.126.20.38713000.673168.5
3.12-3.277.60.35216490.752187.2
3.27-3.4490.31818770.841197.9
3.44-3.659.90.22619140.936199.7
3.65-3.9410.20.1619191.0961100
3.94-4.3310.10.12119471.1421100
4.33-4.969.60.09719361.016199.3
4.96-6.249.90.09220011.081100
6.24-508.90.07521560.97199.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2.906→47.037 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 890 5.08 %
Rwork0.2393 16628 -
obs0.2409 17518 90.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.91 Å2 / Biso mean: 79.3821 Å2 / Biso min: 29.34 Å2
Refinement stepCycle: final / Resolution: 2.906→47.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 42 0 2833
Biso mean--120.65 --
Num. residues----371
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1070X-RAY DIFFRACTION10.844TORSIONAL
12B1070X-RAY DIFFRACTION10.844TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.906-3.08750.3644930.2737164355
3.0875-3.32590.2811460.2467257686
3.3259-3.66050.24861870.229296899
3.6605-4.18980.2581420.20893045100
4.1898-5.27760.25221650.20213090100
5.2776-47.0370.29731570.28913306100
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)
14.9492-2.0052-0.13634.71364.35415.6505-0.3725-0.2903-0.5473-0.58990.1250.6680.6912-1.9607-0.25770.1808-0.1040.05681.16340.09040.672916.21018.481316.2243
21.93481.93040.07643.2905-1.19286.57990.56440.2858-0.15940.29450.30070.17671.1658-1.4331-0.16830.04510.04750.0860.8590.00570.335422.96512.426115.9795
33.90571.38712.30982.30082.17983.5330.6340.5297-0.3620.3443-0.53630.18570.09842.2266-0.14070.6441-0.25480.10050.59420.16910.354424.638412.567426.3408
41.1117-0.92860.60281.23840.61281.529-0.05820.16330.1239-0.1965-0.4674-0.6601-0.68590.2854-0.09440.47990.07720.17810.43780.06640.46121.137629.373428.6336
54.57241.4447-0.97825.8638-2.06333.5734-1.70880.4871.19890.17720.69650.9587-1.2084-1.4632-1.72270.7754-0.3488-0.32190.33350.18140.61367.882727.71755.3347
63.29410.92680.07724.8769-0.73135.4888-0.1979-0.2019-0.0961-0.0212-0.0552-0.6707-0.06111.04880.22390.7607-0.05210.06060.3526-0.05740.532821.187734.800944.9763
71.5539-0.1586-0.55025.09480.79482.63260.3754-0.60750.0560.7873-0.27210.3147-0.87660.01760.13441.0542-0.00610.0060.4021-0.01330.526113.274741.931960.9321
83.194-0.30330.11185.7246-0.17133.82590.09950.37020.27860.7094-0.399-0.3293-1.81150.06670.01540.96280.1331-0.14520.2557-0.02950.422316.44745.871153.0353
92.06612.20310.46014.4237-0.53451.76380.2729-0.59170.85580.27540.39940.3182-0.0308-0.26110.90951.58310.0416-0.00360.362-0.12390.570516.83552.492858.6641
103.1059-0.59790.02181.3262-0.60914.4587-0.11710.20280.32690.20510.2947-0.0822-0.99890.628-0.16060.8212-0.1090.06540.30730.09340.43724.405613.560749.6736
112.628-0.73370.76630.8065-0.13867.1712-0.05160.01060.12010.30110.66740.10640.1632-1.5238-0.10450.4122-0.0937-0.09920.3363-0.15630.38135.909219.006533.8999
125.47180.70231.80811.9469-0.65535.06560.230.0914-0.00840.0924-0.1160.13280.1115-0.5194-0.09910.3125-0.0263-0.00980.7892-0.02330.4227-7.468719.053615.6153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 33 )A13 - 33
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 46 )A34 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 69 )A47 - 69
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 154 )A70 - 154
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 183 )A155 - 183
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 210 )A184 - 210
8X-RAY DIFFRACTION8chain 'A' and (resid 211 through 261 )A211 - 261
9X-RAY DIFFRACTION9chain 'A' and (resid 262 through 277 )A262 - 277
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 46 )B0 - 46
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 156 )B47 - 156
12X-RAY DIFFRACTION12chain 'B' and (resid 157 through 277 )B157 - 277

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