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- PDB-8sdp: HTRA-1 PDSA bound to CKP 3A7 -

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Basic information

Entry
Database: PDB / ID: 8sdp
TitleHTRA-1 PDSA bound to CKP 3A7
Components
  • Cysteine knot peptide 3A7
  • Serine protease HTRA1
KeywordsPEPTIDE BINDING PROTEIN / Protease / Complex / Cysteine Knot peptide
Function / homology
Function and homology information


chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development ...chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development / collagen-containing extracellular matrix / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily ...Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain / Kazal domain / Kazal domain profile. / Growth factor receptor cysteine-rich domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
Ecballium elaterium (jumping cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsUltsch, M.H. / Kirchhofer, D. / Wei, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HTRA-1 PDSA bound to CKP 3A7
Authors: Ultsch, M.H.
History
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease HTRA1
B: Serine protease HTRA1
C: Serine protease HTRA1
I: Cysteine knot peptide 3A7
X: Cysteine knot peptide 3A7
Y: Cysteine knot peptide 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7917
Polymers90,6956
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-79 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.270, 86.790, 199.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine protease HTRA1 / High-temperature requirement A serine peptidase 1 / L56 / Serine protease 11


Mass: 26060.838 Da / Num. of mol.: 3 / Mutation: S328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 DE3
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Cysteine knot peptide 3A7


Mass: 4170.712 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Ecballium elaterium (jumping cucumber)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.67 % / Description: Blocks
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 15% PEG 20000, 0.1M HEPES pH 7.5 / PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→46.92 Å / Num. obs: 11508 / % possible obs: 90.5 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.114 / Net I/σ(I): 13
Reflection shellResolution: 2.87→2.98 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 576 / CC1/2: 0.636 / Rrim(I) all: 1.45 / % possible all: 64.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→46.92 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 583 5.09 %
Rwork0.2762 --
obs0.2774 11456 57.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 5 0 4826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034916
X-RAY DIFFRACTIONf_angle_d0.5696740
X-RAY DIFFRACTIONf_dihedral_angle_d11.5291601
X-RAY DIFFRACTIONf_chiral_restr0.046818
X-RAY DIFFRACTIONf_plane_restr0.004886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.160.4907130.5038296X-RAY DIFFRACTION6
3.16-3.620.3934800.36821505X-RAY DIFFRACTION32
3.62-4.560.32912270.30674168X-RAY DIFFRACTION88
4.56-46.920.26622630.24824904X-RAY DIFFRACTION100
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)
13.82770.5434-1.29695.11140.22674.79270.2743-0.1750.28040.07880.0557-0.2212-0.9319-0.0740.01860.51870.03860.14320.54980.08090.62218.3369-13.4764-22.3547
22.2757-0.49330.85691.3075-1.52915.70390.0257-0.0297-0.51740.02330.179-0.10180.9159-0.42940.00450.7486-0.2334-0.19290.5726-0.02080.70435.6206-45.2493-10.5599
32.6749-2.1953-0.71913.56691.05093.53410.15390.478-0.3375-1.1875-0.07160.03320.3481-0.53710.00060.9324-0.1571-0.15030.796-0.05280.53048.0988-39.7121-45.0328
40.4178-0.20490.26350.321-0.06650.17520.81110.598-0.22620.1524-0.5018-1.0392-0.05350.63950.01080.7247-0.16040.34021.0617-0.06451.066326.1957-16.8853-31.9054
50.62310.1237-0.3390.2036-0.28130.4320.2253-0.02010.616-0.36830.1089-0.3322-0.37260.4926-00.762-0.1568-0.07490.805-0.06440.947622.6339-36.6129-5.8047
60.53160.57110.33382.80360.39820.347-0.49-1.12190.01921.9724-0.9968-1.43831.15970.7041-0.11461.03290.2799-0.06061.201-0.17321.190224.1159-49.2128-35.6529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 164 through 371)
2X-RAY DIFFRACTION2(chain 'B' and resid 165 through 369)
3X-RAY DIFFRACTION3(chain 'C' and resid 164 through 370)
4X-RAY DIFFRACTION4(chain 'I' and resid 4 through 35)
5X-RAY DIFFRACTION5(chain 'X' and resid 4 through 35)
6X-RAY DIFFRACTION6(chain 'Y' and resid 3 through 35)

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