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- PDB-3nzi: Substrate induced remodeling of the active site regulates HtrA1 a... -

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Basic information

Entry
Database: PDB / ID: 3nzi
TitleSubstrate induced remodeling of the active site regulates HtrA1 activity
Components
  • Citrate synthase
  • Serine protease HTRA1
Keywordshydrolase/hydrolase substrate / serine protease / DegP / HtrA / protease / hydrolase-peptide inhibitor complex / hydrolase-hydrolase substrate complex
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / acyltransferase activity, acyl groups converted into alkyl on transfer / citrate (Si)-synthase / chorionic trophoblast cell differentiation / : / citrate metabolic process / programmed cell death / Mitochondrial protein degradation / growth factor binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...Citric acid cycle (TCA cycle) / acyltransferase activity, acyl groups converted into alkyl on transfer / citrate (Si)-synthase / chorionic trophoblast cell differentiation / : / citrate metabolic process / programmed cell death / Mitochondrial protein degradation / growth factor binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / negative regulation of BMP signaling pathway / tricarboxylic acid cycle / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / placenta development / negative regulation of transforming growth factor beta receptor signaling pathway / : / carbohydrate metabolic process / positive regulation of apoptotic process / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Citrate synthase, eukaryotic-type / 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 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / PDZ domain 6 ...Citrate synthase, eukaryotic-type / 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 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Citrate synthase / Serine protease HTRA1 / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTruebestein, L. / Tennstaedt, A. / Hauske, P. / Krojer, T. / Kaiser, M. / Clausen, T. / Ehrmann, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Substrate-induced remodeling of the active site regulates human HTRA1 activity.
Authors: Truebestein, L. / Tennstaedt, A. / Monig, T. / Krojer, T. / Canellas, F. / Kaiser, M. / Clausen, T. / Ehrmann, M.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_atom_id / _struct_ref_seq_dif.details
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease HTRA1
B: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)37,5362
Polymers37,5362
Non-polymers00
Water00
1
A: Serine protease HTRA1
B: Citrate synthase

A: Serine protease HTRA1
B: Citrate synthase

A: Serine protease HTRA1
B: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)112,6076
Polymers112,6076
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9560 Å2
ΔGint-57 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.965, 105.965, 118.336
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Serine protease HTRA1 / L56 / Serine protease 11


Mass: 36685.902 Da / Num. of mol.: 1 / Fragment: unp residues 158-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Citrate synthase


Mass: 849.865 Da / Num. of mol.: 1 / Fragment: unp residues 371-377 / Source method: obtained synthetically / Details: peptidyl boronic acid inhibitor / References: UniProt: Q80X68, UniProt: Q9CZU6*PLUS
Has protein modificationY

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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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0M LiSO4, 0.1M Sodium citrate, 0.5M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9102
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9102 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. all: 12884 / Num. obs: 12884 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 81.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCY

1lcy


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.965 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24884 651 5.1 %RANDOM
Rwork0.20003 ---
obs0.20238 12208 99.98 %-
all-12208 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.371 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å21.45 Å20 Å2
2--2.91 Å20 Å2
3----4.36 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 0 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221660
X-RAY DIFFRACTIONr_bond_other_d0.0010.021104
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9762250
X-RAY DIFFRACTIONr_angle_other_deg0.83932723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56824.84464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.789157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 60 -
Rwork0.283 889 -
obs--100 %

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