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- PDB-1ywh: crystal structure of urokinase plasminogen activator receptor -

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Basic information

Entry
Database: PDB / ID: 1ywh
Titlecrystal structure of urokinase plasminogen activator receptor
Components
  • Urokinase plasminogen activator surface receptorUrokinase receptor
  • antagonist peptide
KeywordsHYDROLASE RECEPTOR / uPAR / three-finger fold / protein-peptide complex
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 ...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 / plasma membrane => GO:0005886 / 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 / membrane => GO:0016020 / 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
Urokinase plasminogen activator surface receptor / 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 / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Urokinase plasminogen activator surface receptor / Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLlinas, P. / Le Du, M.H. / Gardsvoll, H. / Dano, K. / Ploug, M. / Gilquin, B. / Stura, E.A. / Menez, A.
CitationJournal: EMBO J. / Year: 2005
Title: Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide
Authors: Llinas, P. / Le Du, M.H. / Gardsvoll, H. / Dano, K. / Ploug, M. / Gilquin, B. / Stura, E.A. / Menez, A.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase plasminogen activator surface receptor
B: antagonist peptide
C: Urokinase plasminogen activator surface receptor
D: antagonist peptide
E: Urokinase plasminogen activator surface receptor
F: antagonist peptide
G: Urokinase plasminogen activator surface receptor
H: antagonist peptide
I: Urokinase plasminogen activator surface receptor
J: antagonist peptide
K: Urokinase plasminogen activator surface receptor
L: antagonist peptide
M: Urokinase plasminogen activator surface receptor
N: antagonist peptide
O: Urokinase plasminogen activator surface receptor
P: antagonist peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,70866
Polymers290,54416
Non-polymers14,16450
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49430 Å2
ΔGint-331 kcal/mol
Surface area102640 Å2
MethodPISA
2
A: Urokinase plasminogen activator surface receptor
B: antagonist peptide
C: Urokinase plasminogen activator surface receptor
D: antagonist peptide
E: Urokinase plasminogen activator surface receptor
F: antagonist peptide
G: Urokinase plasminogen activator surface receptor
H: antagonist peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,45335
Polymers145,2728
Non-polymers6,18127
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: Urokinase plasminogen activator surface receptor
J: antagonist peptide
K: Urokinase plasminogen activator surface receptor
L: antagonist peptide
M: Urokinase plasminogen activator surface receptor
N: antagonist peptide
O: Urokinase plasminogen activator surface receptor
P: antagonist peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,25431
Polymers145,2728
Non-polymers7,98223
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.928, 136.831, 140.536
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Protein
Urokinase plasminogen activator surface receptor / Urokinase receptor / uPAR / U- PAR / Monocyte activation antigen Mo3 / CD87 antigen


Mass: 34687.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAUR, MO3, UPAR / Plasmid: pMTC-suPAR / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9UMV0, UniProt: Q03405*PLUS
#2: Protein/peptide
antagonist peptide


Mass: 1630.884 Da / Num. of mol.: 8 / Source method: obtained synthetically

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Sugars , 5 types, 29 molecules

#3: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-6-deoxy-Altp]{}}}LINUCSPDB-CARE
#4: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-D-6-deoxy-Altp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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

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Non-polymers , 2 types, 770 molecules

#8: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium sulfate, imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 20K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2002
RadiationMonochromator: Toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→24.85 Å / Num. obs: 110121 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.09 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.769 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.61 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→24.85 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.829 / SU B: 24.952 / SU ML: 0.295 / Cross valid method: OMIT MAPs / σ(F): 0 / ESU R: 0.56 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31526 5335 5 %RANDOM
Rwork0.24524 ---
all0.24876 106866 --
obs0.24876 101531 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.796 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.12 Å2
2---0.17 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16900 0 903 749 18552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02118234
X-RAY DIFFRACTIONr_angle_refined_deg1.6342.0124710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.87652161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62524.477822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.192152978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.17615119
X-RAY DIFFRACTIONr_chiral_restr0.1120.22783
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213187
X-RAY DIFFRACTIONr_nbd_refined0.2320.27785
X-RAY DIFFRACTIONr_nbtor_refined0.3110.211892
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2896
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.25
X-RAY DIFFRACTIONr_mcbond_it0.4971.511031
X-RAY DIFFRACTIONr_mcangle_it0.94217351
X-RAY DIFFRACTIONr_scbond_it1.32737792
X-RAY DIFFRACTIONr_scangle_it2.1884.57359
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 375 -
Rwork0.291 7572 -
obs--99.33 %

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