[English] 日本語
Yorodumi
- PDB-1g2z: DIMERIZATION DOMAIN OF HNF-1ALPHA WITH A LEU 13 SELENOMETHIONINE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g2z
TitleDIMERIZATION DOMAIN OF HNF-1ALPHA WITH A LEU 13 SELENOMETHIONINE SUBSTITUTION
ComponentsHEPATOCYTE NUCLEAR FACTOR 1-ALPHA
KeywordsTRANSCRIPTION / dimerization domain / four-helix bundle / transcription factor / selenomethionine
Function / homology
Function and homology information


paraxial mesoderm formation / cellular response to rapamycin / apoptotic nuclear changes / regulation of NADP metabolic process / renal glucose absorption / regulation of hormone secretion / reproductive structure development / cellular response to L-leucine / bile acid biosynthetic process / reverse cholesterol transport ...paraxial mesoderm formation / cellular response to rapamycin / apoptotic nuclear changes / regulation of NADP metabolic process / renal glucose absorption / regulation of hormone secretion / reproductive structure development / cellular response to L-leucine / bile acid biosynthetic process / reverse cholesterol transport / pronucleus / bile acid and bile salt transport / regulation of Wnt signaling pathway / pancreas development / negative regulation of miRNA processing / positive regulation of mitochondrial membrane potential / embryonic limb morphogenesis / insulin secretion / heme biosynthetic process / positive regulation of ATP biosynthetic process / negative regulation of peptidyl-threonine phosphorylation / glucose import / blastocyst development / photoreceptor outer segment / fatty acid transport / response to glucose / bone resorption / cholesterol metabolic process / liver development / transcription coregulator binding / cellular response to glucose stimulus / placenta development / protein localization / positive regulation of insulin secretion / transcription coactivator binding / fatty acid biosynthetic process / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus ...Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Hepatocyte nuclear factor 1-alpha
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsRose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T.
Citation
Journal: Biochemistry / Year: 2000
Title: High-resolution structure of the HNF-1alpha dimerization domain.
Authors: Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha
Authors: Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T.
History
DepositionOct 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)6,9042
Polymers6,9042
Non-polymers00
Water1,78399
1
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)13,8084
Polymers13,8084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4680 Å2
ΔGint-53 kcal/mol
Surface area7470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.100, 41.200, 42.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTwo monomers are in the asymmetric unit, although not the biologically relevant dimer. The dimer of each of the monomers is generated by the two fold axis: -x+2, -y, z.

-
Components

#1: Protein/peptide HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / HNF-1A / LIVER SPECIFIC TRANSCRIPTION FACTOR LF-B1


Mass: 3451.884 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 1-32 / Mutation: L13(MSE) / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in mouse (Mus musculus), with a point mutation at position 13.
References: UniProt: P22361
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris-HCl, lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlpeptide1drop
230 %PEG40001reservoir
3100 mMTris-HCl1reservoir
40.2 M1reservoirLiSO4

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.95372, 0.97957, 0.9798, 1.00
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 1999 / Details: Double crystal
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
20.979571
30.97981
411
ReflectionResolution: 1.15→29.5 Å / Num. all: 22638 / Num. obs: 22638 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.2
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2032 / % possible all: 90
Reflection
*PLUS
Num. obs: 31540 / % possible obs: 93 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Highest resolution: 1.05 Å / Lowest resolution: 1.11 Å / % possible obs: 82.1 % / Rmerge(I) obs: 0.398

-
Processing

Software
NameVersionClassification
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD
Starting model: wARP model

Resolution: 1.15→29.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 563662.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement carried out in tnt. Statistics reported from CNS (input file: model_stats.list).
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1124 5 %RANDOM
Rwork0.216 ---
all0.216 22638 --
obs0.216 22638 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 97.28 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2--0.783 Å20 Å2
3---0.869 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.15→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms462 0 0 99 561
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.369
X-RAY DIFFRACTIONc_dihedral_angle_d17.79
X-RAY DIFFRACTIONc_improper_angle_d4.631.5
X-RAY DIFFRACTIONc_mcbond_it10.572
X-RAY DIFFRACTIONc_mcangle_it9.722
X-RAY DIFFRACTIONc_scbond_it19.462.5
X-RAY DIFFRACTIONc_scangle_it21.7
LS refinement shellResolution: 1.15→1.19 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 100 5.3 %
Rwork0.35 3970 -
obs-2032 90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Num. reflection Rfree: 1443 / % reflection Rfree: 5 % / Rfactor obs: 0.223 / Rfactor Rfree: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.79
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.631.5
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_mcangle_it2
LS refinement shell
*PLUS
Rfactor Rfree: 0.31 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.35

+
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://pdbjlvh1.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