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- PDB-5h7v: Structure of full-length extracellular domain of HAI-1 at pH 4.6 -

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Basic information

Entry
Database: PDB / ID: 5h7v
TitleStructure of full-length extracellular domain of HAI-1 at pH 4.6
ComponentsKunitz-type protease inhibitor 1
KeywordsHYDROLASE INHIBITOR / HAI-1
Function / homology
Function and homology information


epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / extracellular matrix organization ...epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / extracellular matrix organization / neural tube closure / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / MANSC domain profile. / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. ...MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / MANSC domain profile. / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / Immunoglobulin-like fold
Similarity search - Domain/homology
Kunitz-type protease inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.82 Å
AuthorsLiu, M. / Huang, M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The crystal structure of a multidomain protease inhibitor (HAI-1) reveals the mechanism of its auto-inhibition
Authors: Liu, M. / Yuan, C. / Jensen, J.K. / Zhao, B. / Jiang, Y. / Jiang, L. / Huang, M.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kunitz-type protease inhibitor 1


Theoretical massNumber of molelcules
Total (without water)47,2961
Polymers47,2961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.620, 95.620, 124.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Kunitz-type protease inhibitor 1 / Hepatocyte growth factor activator inhibitor type 1 / HAI-1


Mass: 47295.848 Da / Num. of mol.: 1 / Fragment: ligand binding region, UNP residues 36-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINT1, HAI1, UNQ223/PRO256 / Plasmid: PMT/BIP / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 Cells / References: UniProt: O43278

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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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.6M ammonium sulfate, 20% (v/v) glycerol, 0.08M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.82→38.09 Å / Num. obs: 5987 / % possible obs: 99.98 % / Redundancy: 25.2 % / Net I/σ(I): 17.47

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MSX

2msx


Resolution: 3.82→38.09 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3281 287 4.79 %
Rwork0.2527 --
obs0.2563 5986 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 346.54 Å2 / Biso mean: 170.905 Å2 / Biso min: 69.27 Å2
Refinement stepCycle: final / Resolution: 3.82→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 0 2489
Num. residues----320
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)
18.64673.64986.86389.73583.46645.4940.31510.3043-1.9656-1.21521.2271-1.9637-0.6798-0.10260.67060.51270.23570.88162.34220.91381.5995-42.544227.7576-18.8125
24.90923.539-1.99515.6038-0.44311.01181.1799-1.81460.1521-1.0431-1.52120.275-0.18350.10470.12581.06660.02130.09141.4767-0.00970.9997-23.777534.7322-10.4763
35.7998-0.77165.1284.7873-3.2286.60241.95262.04330.66550.1763-0.26261.7462-0.3154-0.7049-1.47951.24490.33440.1951.63820.57021.729-33.069535.572-18.6638
44.80961.4862-0.47214.0636-0.61660.10940.0812-0.64721.71680.82390.6401-0.4553-0.62060.4539-0.14133.90010.71421.5181.1086-0.52062.8347-38.512449.1447-9.517
56.32354.6984-0.54743.4734-0.40677.07570.9996-0.1370.617-0.375-0.753-0.8037-0.6241-1.2881-0.65120.66060.04430.06051.0949-0.03860.8544-24.264731.9554-12.2854
64.47810.68790.96822.2064-2.21782.8991-0.1016-0.42240.60230.97880.50141.0629-0.1298-1.1088-0.40191.00570.38850.04071.47410.01940.6893-30.61132.227-7.6466
70.722-1.6084-2.5045.55253.90751.99060.3116-2.6231-3.03210.6441-1.043-1.69274.1024-0.2399-0.16021.09950.2783-0.24273.00521.23361.696-25.733921.14830.8285
81.9835-4.2155-6.73963.75261.26615.15680.41352.7104-1.2967-1.1791-1.07652.3520.109-1.51830.49161.2815-0.3173-0.43351.5630.46831.611-7.650212.494-17.0102
98.1145-3.52766.94213.14490.46292.0036-0.9887-0.0691-1.4776-1.92461.75230.23133.60510.2915-0.36341.0138-0.81790.16192.26280.43381.266-8.31025.8228-6.0382
103.2164-2.93341.14974.50811.42313.94571.0917-1.07241.5220.186-2.46230.35082.9347-0.91690.51441.6714-0.0321-0.26211.45850.36942.5087-10.34020.2194-16.0588
117.3391-5.2368-0.31494.66540.45112.7282-0.3696-0.3268-1.01880.6509-0.06734.46141.4302-1.18270.09021.8131-0.13130.33581.33670.09742.0408-7.01165.2415-15.3677
123.19251.6762-1.18943.5173-4.66246.62170.1408-0.61791.0387-0.14050.9951-1.18352.4022-1.6271.3322.7701-1.46891.20023.6233-2.26563.4238-16.39725.7425-3.3017
130.696-2.2327-1.2587.22074.05522.27872.0669-1.48231.8799-1.34171.3606-0.3102-0.0299-1.1371-1.71371.1804-0.1475-0.0392.4153-0.27340.5751-12.876213.3616-20.6109
149.287-0.777-7.28483.2339-1.75677.4725-4.19353.5741-1.2982-1.76362.5198-0.4638-1.7343-0.15550.4061.5527-0.5605-0.29281.505-0.35971.2231-7.060324.2458-27.9241
153.60215.52734.65978.92686.00279.0127-0.39151.5083-0.41680.12212.61340.8938-0.36231.22532.82181.2894-0.2789-0.73981.590.85861.9775-11.671841.4578-22.9676
164.6111.15463.4645.14670.32139.1850.34340.5640.1886-1.67331.01892.14041.09210.8143-1.41481.0276-0.1379-0.22461.21510.11221.2856-3.637827.9318-19.696
174.5774-3.60092.11272.02075.28946.2237-2.6985-0.2379-0.482.161-1.18361.7470.51270.37532.77922.84320.8431-0.0111.39880.1021.3454-13.991928.9203-32.2175
185.43420.74624.99193.0141.30634.70470.1886-2.7347-1.3710.6136-1.1581-0.87030.05742.5485-1.75620.2472-0.15341.07221.32420.54312.3315-20.96444.0607-24.6133
191.4929-0.8469-0.82580.8911-1.63039.39411.0051-1.2685-0.3421-0.1196-0.4855-1.036-1.06531.8673-0.50691.1231-0.1084-0.14251.4751-0.2881.3665-18.270537.6637-0.329
203.0532-5.04861.69558.3397-1.978.0113-0.2951-1.19291.50340.70891.4228-1.7905-0.2458-1.5696-1.03221.3139-0.3185-0.20722.882-0.39281.7438-11.427727.27238.676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 45:53)A45 - 53
2X-RAY DIFFRACTION2(chain A and resid 54:77)A54 - 77
3X-RAY DIFFRACTION3(chain A and resid 78:104)A78 - 104
4X-RAY DIFFRACTION4(chain A and resid 105:110)A105 - 110
5X-RAY DIFFRACTION5(chain A and resid 111:132)A111 - 132
6X-RAY DIFFRACTION6(chain A and resid 133:147)A133 - 147
7X-RAY DIFFRACTION7(chain A and resid 148:154)A148 - 154
8X-RAY DIFFRACTION8(chain A and resid 166:179)A166 - 179
9X-RAY DIFFRACTION9(chain A and resid 180:191)A180 - 191
10X-RAY DIFFRACTION10(chain A and resid 192:203)A192 - 203
11X-RAY DIFFRACTION11(chain A and resid 204:220)A204 - 220
12X-RAY DIFFRACTION12(chain A and resid 221:233)A221 - 233
13X-RAY DIFFRACTION13(chain A and resid 234:244)A234 - 244
14X-RAY DIFFRACTION14(chain A and resid 245:254)A245 - 254
15X-RAY DIFFRACTION15(chain A and resid 255:260)A255 - 260
16X-RAY DIFFRACTION16(chain A and resid 261:303)A261 - 303
17X-RAY DIFFRACTION17(chain A and resid 304:358)A304 - 358
18X-RAY DIFFRACTION18(chain A and resid 359:365)A359 - 365
19X-RAY DIFFRACTION19(chain A and resid 366:380)A366 - 380
20X-RAY DIFFRACTION20(chain A and resid 381:425)A381 - 425

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