[English] 日本語
Yorodumi
- PDB-1zwa: STRUCTURE OF HUMAN PARATHYROID HORMONE FRAGMENT 1-34, NMR, 10 STR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zwa
TitleSTRUCTURE OF HUMAN PARATHYROID HORMONE FRAGMENT 1-34, NMR, 10 STRUCTURES
ComponentsPARATHYROID HORMONE
KeywordsHORMONE / DISEASE MUTATION
Function / homology
Function and homology information


parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / macromolecule biosynthetic process / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis ...parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / macromolecule biosynthetic process / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis / positive regulation of signal transduction / response to fibroblast growth factor / phosphate ion homeostasis / cAMP metabolic process / response to vitamin D / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / bone mineralization / Rho protein signal transduction / positive regulation of glycogen biosynthetic process / bone resorption / positive regulation of bone mineralization / response to cadmium ion / homeostasis of number of cells within a tissue / skeletal system development / positive regulation of D-glucose import / response to lead ion / hormone activity / intracellular calcium ion homeostasis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell signaling / regulation of gene expression / G alpha (s) signalling events / response to ethanol / transcription by RNA polymerase II / G protein-coupled receptor signaling pathway / receptor ligand activity / response to xenobiotic stimulus / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsRoesch, P. / Marx, U.C.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2000
Title: Solution structures of human parathyroid hormone fragments hPTH(1-34) and hPTH(1-39) and bovine parathyroid hormone fragment bPTH(1-37).
Authors: Marx, U.C. / Adermann, K. / Bayer, P. / Forssmann, W.G. / Rosch, P.
#1: Journal: Thesis, University of Bayreuth / Year: 1996
Title: Strukturen Verschiedener Parathormonfragmente in Loesung
Authors: Marx, U.C.
History
DepositionJun 17, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PARATHYROID HORMONE


Theoretical massNumber of molelcules
Total (without water)4,1261
Polymers4,1261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -
Representative

-
Components

#1: Protein/peptide PARATHYROID HORMONE / HPTH(1-34)


Mass: 4125.778 Da / Num. of mol.: 1 / Fragment: 1 - 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / References: UniProt: P01270

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 10

+
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