[English] 日本語
Yorodumi
- PDB-2joa: HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2joa
TitleHtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances
Components
  • Peptide H1-C1
  • Serine protease HTRA1
KeywordsPROTEIN BINDING / PDZ / beta-sandwich / cyclically-permuted
Function / homology
Function and homology information


chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / negative regulation of BMP signaling pathway / 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 / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / negative regulation of BMP signaling pathway / 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 / : / 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. / PDZ domain / Pdz3 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 / Roll / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRunyon, S.T. / Zhang, Y. / Appleton, B.A. / Sazinksy, S.L. / Wu, P. / Pan, B. / Wiesmann, C. / Skelton, N.J. / Sidhu, S.S.
Citation
Journal: Protein Sci. / Year: 2007
Title: Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3
Authors: Runyon, S.T. / Zhang, Y. / Appleton, B.A. / Sazinsky, S.L. / Wu, P. / Pan, B. / Wiesmann, C. / Skelton, N.J. / Sidhu, S.S.
#1: Journal: To be Published
Title: HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances
Authors: Runyon, S.T. / Pan, B. / Skelton, N.J.
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease HTRA1
B: Peptide H1-C1


Theoretical massNumber of molelcules
Total (without water)12,5442
Polymers12,5442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1090 Å2
ΔGint-6 kcal/mol
Surface area7330 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

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


Mass: 11582.238 Da / Num. of mol.: 1 / Fragment: PDZ domain, residues 379-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Peptide H1-C1


Mass: 962.083 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The peptide was derived from a phage-displayed library as an optimal ligand for binding to the PDZ domain of human HtrA1.
Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D HNCO
1423D HN(CA)CB
1523D CBCA(CO)NH
1623D HN(CO)CA
1742D 1H-13C HSQC
1813D 1H-15N NOESY
1933D 1H-13C NOESY
11033D (H)CCH-TOCSY
11152D 1H-1H NOESY 13C,15N-filtered in F1
11252D 1H-1H TOCSY,13C,15N-filtered in F1
11363D 1H-13C NOESY, 13C-filtered in F1

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1, 90% H2O/10% D2O90% H2O/10% D2O
32 mM [U-13C; U-15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1, 100% D2O100% D2O
42 mM [U-10% 13C; U-99% 15N] HtrA1-PDZ, 4 mM synthetic peptide H1-C1, 100% D2O100% D2O
52 mM [U-13C; U-15N] HtrA1-PDZ, 1.8 mM synthetic peptide H1-C1, 90% H2O/10% D2O90% H2O/10% D2O
62 mM [U-13C; U-15N] HtrA1-PDZ, 1.8 mM synthetic peptide H1-C1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMHtrA1-PDZ[U-15N]1
4 mMsynthetic peptide H1-C11
2 mMHtrA1-PDZ[U-13C; U-15N]2
4 mMsynthetic peptide H1-C12
2 mMHtrA1-PDZ[U-13C; U-15N]3
4 mMsynthetic peptide H1-C13
2 mMHtrA1-PDZ[U-10% 13C; U-99% 15N]4
4 mMsynthetic peptide H1-C14
2 mMHtrA1-PDZ[U-13C; U-15N]5
1.8 mMsynthetic peptide H1-C15
2 mMHtrA1-PDZ[U-13C; U-15N]6
1.8 mMsynthetic peptide H1-C16
Sample conditionsIonic strength: 0.025 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2005 for LINUXDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddarddata analysis
Monte2.02Hitchens, T.K., Lukin, J.A., Zhan, Y. and Rule, G.S.chemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichautomated noe assignment
TopSpin1.3Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
CNX2002Accelrys Software Inc.structure solution
CNX2002Accelrys Software Inc.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: followed by cartesian dynamics and minimization
NMR constraintsNOE constraints total: 1352 / NOE intraresidue total count: 179 / NOE long range total count: 504 / NOE medium range total count: 252 / NOE sequential total count: 340 / Hydrogen bond constraints total count: 42 / Protein chi angle constraints total count: 21 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 77 / Protein psi angle constraints total count: 76
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.9 ° / Maximum upper distance constraint violation: 0.08 Å / Torsion angle constraint violation method: CNX
NMR ensemble rmsDistance rms dev: 0.0049 Å / Distance rms dev error: 0.0008 Å

+
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