[English] 日本語
Yorodumi
- PDB-1huw: THE CRYSTAL STRUCTURE OF AFFINITY-MATURED HUMAN GROWTH HORMONE AT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1huw
TitleTHE CRYSTAL STRUCTURE OF AFFINITY-MATURED HUMAN GROWTH HORMONE AT 2 ANGSTROMS RESOLUTION
ComponentsHUMAN GROWTH HORMONE
KeywordsHORMONE
Function / homology
Function and homology information


growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / animal organ development / positive regulation of multicellular organism growth / growth hormone receptor binding / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / positive regulation of insulin-like growth factor receptor signaling pathway ...growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / animal organ development / positive regulation of multicellular organism growth / growth hormone receptor binding / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor signaling pathway / Prolactin receptor signaling / growth hormone receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / positive regulation of MAP kinase activity / cytokine activity / endosome lumen / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to nutrient levels / cytokine-mediated signaling pathway / hormone activity / response to estradiol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsUltsch, M.H. / Somers, W.S. / Kossiakoff, A.A. / De Vos, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The crystal structure of affinity-matured human growth hormone at 2 A resolution.
Authors: Ultsch, M.H. / Somers, W. / Kossiakoff, A.A. / de Vos, A.M.
#1: Journal: To be Published
Title: Affinity Maturation of Human Growth Hormone by Monovalent Phage Display
Authors: Lowman, H.B. / Wells, J.A.
History
DepositionSep 22, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN GROWTH HORMONE


Theoretical massNumber of molelcules
Total (without water)21,9871
Polymers21,9871
Non-polymers00
Water1,38777
1
A: HUMAN GROWTH HORMONE

A: HUMAN GROWTH HORMONE


Theoretical massNumber of molelcules
Total (without water)43,9732
Polymers43,9732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Unit cell
Length a, b, c (Å)80.450, 59.340, 50.870
Angle α, β, γ (deg.)90.00, 128.20, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein HUMAN GROWTH HORMONE


Mass: 21986.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01241
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoir
46 mg/mlprotein1drop
5120 mM1dropNaCl
620 mMsodium cacoylate1drop
75.0 mMEDTA1drop
81 mMphenylmethylsulfonyl fluoride1drop
910 %(w/v)PEG80001drop
100.2 Mmagnesium acetate1drop
110.1 Msodium cacodylate1drop

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. obs: 6630 / % possible obs: 97.3 % / Num. measured all: 16335 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å / % possible obs: 94.1 % / Num. unique obs: 626 / Num. measured obs: 1167 / Rmerge(I) obs: 0.144

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 77 1438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. reflection all: 12423 / Num. reflection obs: 11341 / σ(F): 2 / Rfactor all: 0.199 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.63
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Num. reflection Rfree: 4151 / Rfactor obs: 0.298

+
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