[English] 日本語
Yorodumi
- PDB-1kf9: PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED W... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kf9
TitlePHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR
Components
  • EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
  • PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
KeywordsHORMONE/GROWTH FACTOR / CYTOKINE / HORMONE-RECEPTOR COMPLEX / PHAGE DISPLAY MOLECULAR PLASTICITY / RECEPTOR HOMODIMERIZATION / HUMAN GROWTH HORMONE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of response to nutrient levels / growth hormone receptor activity / growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / taurine metabolic process / animal organ development / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth ...regulation of response to nutrient levels / growth hormone receptor activity / growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / taurine metabolic process / animal organ development / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / positive regulation of D-glucose transmembrane transport / proline-rich region binding / hormone metabolic process / cell surface receptor signaling pathway via STAT / growth hormone receptor binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor signaling pathway / response to food / growth factor binding / response to cycloheximide / Prolactin receptor signaling / response to gravity / cytokine binding / positive regulation of MAP kinase activity / peptide hormone binding / regulation of multicellular organism growth / 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 / cellular response to hormone stimulus / hormone-mediated signaling pathway / SH2 domain binding / insulin-like growth factor receptor signaling pathway / response to interleukin-1 / response to glucocorticoid / endosome lumen / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of cell differentiation / growth factor activity / response to nutrient levels / hormone activity / receptor internalization / cytoplasmic ribonucleoprotein granule / endocytosis / cellular response to insulin stimulus / cytokine-mediated signaling pathway / response to estradiol / protein phosphatase binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / external side of plasma membrane / neuronal cell body / positive regulation of cell population proliferation / lipid binding / protein kinase binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Growth hormone-binding protein / Growth hormone receptor binding / Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding ...Growth hormone-binding protein / Growth hormone receptor binding / Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Somatotropin / Growth hormone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchiffer, C.A. / Ultsch, M. / Walsh, S. / Somers, W. / De Vos, A.M. / Kossiakoff, A.A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of a Phage Display Derived Variant of Human Growth Hormone Complexed to Two Copies of the Extracellular Domain of its Receptor: Evidence for Strong Structural Coupling between Receptor Binding Sites
Authors: Schiffer, C.A. / Ultsch, M. / Walsh, S. / Somers, W. / De Vos, A.M. / Kossiakoff, A.A.
History
DepositionNov 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence of the molecules A and D have not been deposited in any sequence database.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
B: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
C: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
D: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
E: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
F: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Theoretical massNumber of molelcules
Total (without water)153,6126
Polymers153,6126
Non-polymers00
Water1,33374
1
A: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
B: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
C: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Theoretical massNumber of molelcules
Total (without water)76,8063
Polymers76,8063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-18 kcal/mol
Surface area24750 Å2
MethodPISA
2
D: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
E: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
F: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Theoretical massNumber of molelcules
Total (without water)76,8063
Polymers76,8063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-19 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.289, 111.937, 95.290
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE


Mass: 21986.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01241*PLUS
#2: Protein
EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Mass: 27409.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10912
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growpH: 6.3 / Details: pH 6.30
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium citrate1reservoir
430 %PEG25001reservoirpH6.3

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 43162 / % possible obs: 95.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 215604
Reflection shell
*PLUS
% possible obs: 78.8 %

-
Processing

Software
NameVersionClassification
SCALEdata collection
AUTOMARdata reduction
X-PLORmodel building
X-PLOR3.843refinement
SCALEdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1798 5 %RANDOM 5%
Rwork0.234 ---
obs0.234 39338 90.5 %-
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20.3 Å2
2---5.9 Å20 Å2
3---14.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8604 0 0 74 8678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.8
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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