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- PDB-5hgg: Crystal structure of uPA in complex with a camelid-derived antibo... -

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Basic information

Entry
Database: PDB / ID: 5hgg
TitleCrystal structure of uPA in complex with a camelid-derived antibody fragment
Components
  • Camelid Derived Antibody Fragment, Nb4
  • Urokinase-type plasminogen activator
KeywordsHYDROLASE/INHIBITOR / uPA / Nanobody / Serine Protease / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. ...Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-TWN / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsYung, K.W.Y. / Kromann-Hansen, T. / Andreasen, P.A. / Ngo, J.C.K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior
Authors: Kromann-Hansen, T. / Oldenburg, E. / Yung, K.W. / Ghassabeh, G.H. / Muyldermans, S. / Declerck, P.J. / Huang, M. / Andreasen, P.A. / Ngo, J.C.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
B: Urokinase-type plasminogen activator
S: Camelid Derived Antibody Fragment, Nb4
T: Camelid Derived Antibody Fragment, Nb4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,53915
Polymers82,6274
Non-polymers1,91211
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-65 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.985, 77.749, 61.454
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody , 2 types, 4 molecules ABST

#1: Protein Urokinase-type plasminogen activator / uPA


Mass: 27715.600 Da / Num. of mol.: 2 / Fragment: UNP residues 179-424 / Mutation: C122A, N145Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: P00749, u-plasminogen activator
#2: Antibody Camelid Derived Antibody Fragment, Nb4


Mass: 13597.960 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 298 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TWN / (3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE


Mass: 354.567 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: Sodium Phosphate dibasic, Ammonium Sulfate, MES, Tween 20

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 59384 / % possible obs: 97.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.032 / Rrim(I) all: 0.067 / Χ2: 0.665 / Net I/av σ(I): 19.381 / Net I/σ(I): 8.4 / Num. measured all: 247411
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-23.70.36428040.890.210.4210.47892.6
2-2.043.90.31429150.9210.1780.3620.595.6
2.04-2.0840.29329230.9220.1650.3380.55497.1
2.08-2.124.10.27829190.9340.1560.3190.53396.2
2.12-2.174.20.24329750.9480.1350.2790.5497.4
2.17-2.224.20.21129230.9620.1170.2420.54497.6
2.22-2.274.20.19929520.9630.110.2280.59996.3
2.27-2.344.20.16429600.9750.0910.1870.57398.2
2.34-2.44.20.14529780.9830.080.1660.59897.8
2.4-2.484.30.12229570.9860.0670.1390.58397
2.48-2.574.30.11129560.9880.0610.1270.61997.6
2.57-2.674.30.09830150.9910.0540.1120.63297.9
2.67-2.794.30.08329720.9930.0460.0950.61998.2
2.79-2.944.30.07129830.9950.0390.080.68498.5
2.94-3.134.30.05630010.9970.0310.0640.71998.7
3.13-3.374.20.04330270.9980.0240.0490.80698.9
3.37-3.714.20.03530120.9980.0190.040.83598.5
3.71-4.244.20.03130030.9990.0170.0350.98898.4
4.24-5.344.10.02630190.9990.0140.030.90297.6
5.34-304.10.02530900.9990.0140.0290.92298.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.643 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 2999 5.1 %RANDOM
Rwork0.1673 ---
obs0.1688 56384 97.37 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 135.02 Å2 / Biso mean: 31.205 Å2 / Biso min: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0.47 Å2
2--0.24 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 127 287 6197
Biso mean--68.7 32.36 -
Num. residues----747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196065
X-RAY DIFFRACTIONr_bond_other_d0.0060.025665
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9618193
X-RAY DIFFRACTIONr_angle_other_deg1.241313066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11923.206262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04315993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951544
X-RAY DIFFRACTIONr_chiral_restr0.1290.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026780
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021420
X-RAY DIFFRACTIONr_mcbond_it1.6651.622988
X-RAY DIFFRACTIONr_mcbond_other1.6641.622987
X-RAY DIFFRACTIONr_mcangle_it2.4622.4163724
LS refinement shellResolution: 1.969→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 191 -
Rwork0.225 4014 -
all-4205 -
obs--93.36 %
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)
11.49280.1952-0.33351.90630.33851.94690.01670.1717-0.0879-0.0708-0.12460.21140.0495-0.36990.10790.07090.00920.01880.0978-0.02980.0436200.184-0.69964.168
21.8922-0.23280.28961.8991-0.66361.9852-0.0707-0.03310.29160.08010.090.2354-0.1579-0.3707-0.01930.05280.01460.03310.0981-0.02220.1261185.49237.90192.152
32.2927-0.5796-1.41091.2270.86281.46650.01410.16140.0832-0.1286-0.03450.00070.0186-0.08330.02040.1132-0.0170.02830.02940.01040.0227212.04827.77977.198
40.5715-0.431-0.28171.73171.18623.59840.0471-0.0698-0.02450.1211-0.04130.0642-0.0111-0.1692-0.00580.0688-0.00140.03730.03560.01380.0288202.519.31794.433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 243
2X-RAY DIFFRACTION2B16 - 243
3X-RAY DIFFRACTION3S1 - 128
4X-RAY DIFFRACTION4T1 - 127

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