[English] 日本語
Yorodumi
- PDB-3tjn: HtrA1 catalytic domain, apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tjn
TitleHtrA1 catalytic domain, apo form
ComponentsSerine protease HTRA1
KeywordsHYDROLASE / protease
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 / placenta development / negative regulation of transforming growth factor beta receptor signaling pathway ...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 / placenta development / negative regulation of transforming growth factor beta receptor signaling pathway / 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 / Kazal domain / Kazal domain profile. / Trypsin-like peptidase domain / 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
Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: Structure / Year: 2012
Title: Structural and Functional Analysis of HtrA1 and Its Subdomains.
Authors: Eigenbrot, C. / Ultsch, M. / Lipari, M.T. / Moran, P. / Lin, S.J. / Ganesan, R. / Quan, C. / Tom, J. / Sandoval, W. / van Lookeren Campagne, M. / Kirchhofer, D.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease HTRA1
B: Serine protease HTRA1
D: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water00
1
A: Serine protease HTRA1

A: Serine protease HTRA1

A: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area5730 Å2
ΔGint-22 kcal/mol
Surface area25210 Å2
MethodPISA
2
B: Serine protease HTRA1

B: Serine protease HTRA1

B: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6290 Å2
ΔGint-32 kcal/mol
Surface area26670 Å2
MethodPISA
3
D: Serine protease HTRA1

D: Serine protease HTRA1

D: Serine protease HTRA1


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,2123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6100 Å2
ΔGint-27 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.495, 108.495, 234.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHISAA164 - 18525 - 46
21SERSERHISHISBB164 - 18525 - 46
31SERSERHISHISDC164 - 18525 - 46
12VALVALTHRTHRAA199 - 22360 - 84
22VALVALTHRTHRBB199 - 22360 - 84
32VALVALTHRTHRDC199 - 22360 - 84
13ARGARGGLYGLYAA227 - 28388 - 144
23ARGARGGLYGLYBB227 - 28388 - 144
33ARGARGGLYGLYDC227 - 28388 - 144
14ASNASNTHRTHRAA290 - 300151 - 161
24ASNASNTHRTHRBB290 - 300151 - 161
34ASNASNTHRTHRDC290 - 300151 - 161
15ASPASPILEILEAA315 - 323176 - 184
25ASPASPILEILEBB315 - 323176 - 184
35ASPASPILEILEDC315 - 323176 - 184
16GLYGLYTHRTHRAA330 - 344191 - 205
26GLYGLYTHRTHRBB330 - 344191 - 205
36GLYGLYTHRTHRDC330 - 344191 - 205
17SERSERLYSLYSAA352 - 362213 - 223
27SERSERLYSLYSBB352 - 362213 - 223
37SERSERLYSLYSDC352 - 362213 - 223

-
Components

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


Mass: 24737.268 Da / Num. of mol.: 3 / Fragment: protease domain (UNP residues 161-367)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA, HTRA1, PRSS11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium acetate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 17102 / Num. obs: 16292 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 11 % / Rsym value: 0.077 / Net I/σ(I): 27

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCY

1lcy


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 44.554 / SU ML: 0.372 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): -2 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29372 799 4.7 %RANDOM
Rwork0.2421 ---
obs0.24449 16292 99.85 %-
all-17102 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.021 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.03 Å2-0 Å2
2--2.07 Å2-0 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 0 0 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224446
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9726013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14824.737171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55915795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213210
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4782.52842
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.35554617
X-RAY DIFFRACTIONr_scbond_it2.6992.51604
X-RAY DIFFRACTIONr_scangle_it4.55851396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1098 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.50.5
2BMEDIUM POSITIONAL0.450.5
3DMEDIUM POSITIONAL0.420.5
1AMEDIUM THERMAL19.2850
2BMEDIUM THERMAL5.4150
3DMEDIUM THERMAL21.4650
LS refinement shellResolution: 3→3.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.362 124 -
Rwork0.286 2287 -
obs--99.46 %
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)
10.75830.738-0.18091.7521-0.19730.67420.0431-0.06180.1068-0.01220.0056-0.0252-0.08260.0777-0.04870.1806-0.0194-0.01690.1777-0.03910.2005-43.8365-13.7294-47.0186
21.08970.7525-0.74171.24230.0692.88490.00150.0232-0.1050.0887-0.10010.12510.3116-0.23340.09860.2346-0.08560.03710.1328-0.03350.1952-64.66614.828-31.1187
30.24120.1893-0.68761.061-0.73453.2997-0.053-0.2338-0.03070.2898-0.1809-0.2052-0.19620.30760.23390.3659-0.0826-0.14160.51060.0520.0693-37.2347-21.4334-6.8155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A164 - 367
2X-RAY DIFFRACTION2B163 - 367
3X-RAY DIFFRACTION3D164 - 367

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more