[English] 日本語
Yorodumi
- PDB-1h2l: Factor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragmen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h2l
TitleFactor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragment peptide
Components
  • FACTOR INHIBITING HIF1
  • HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
KeywordsTRANSCRIPTION ACTIVATOR/INHIBITOR / TRANSCRIPTION ACTIVATOR-INHIBITOR COMPLEX / TRANSCRIPTION ACTIVATOR INHIBITOR COMPLEX / OXYGENASE / TRANSCRIPTION / HYPOXIA / ASPARAGINYL HYDROXYLASE / HYDROXYLASE
Function / homology
Function and homology information


positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / peptidyl-aspartic acid 3-dioxygenase activity / positive regulation of hormone biosynthetic process ...positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / peptidyl-aspartic acid 3-dioxygenase activity / positive regulation of hormone biosynthetic process / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / PTK6 Expression / collagen metabolic process / regulation of protein neddylation / positive regulation of vasculogenesis / vascular endothelial growth factor production / carboxylic acid binding / intracellular oxygen homeostasis / ankyrin repeat binding / transcription regulator activator activity / STAT3 nuclear events downstream of ALK signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / motile cilium / positive regulation of cytokine production involved in inflammatory response / Notch binding / negative regulation of ossification / positive regulation of vascular endothelial growth factor receptor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / response to iron ion / oxygen sensor activity / regulation of glycolytic process / DNA-binding transcription repressor activity / PTK6 promotes HIF1A stabilization / Regulation of PD-L1(CD274) transcription / DNA-binding transcription activator activity / axonal transport of mitochondrion / E-box binding / positive regulation of epithelial cell migration / negative regulation of Notch signaling pathway / epithelial to mesenchymal transition / positive regulation of vascular endothelial growth factor production / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / positive regulation of myoblast differentiation / NF-kappaB binding / cis-regulatory region sequence-specific DNA binding / negative regulation of reactive oxygen species biosynthetic process / positive regulation of chemokine production / positive regulation of endothelial cell proliferation / axon cytoplasm / positive regulation of erythrocyte differentiation / negative regulation of miRNA transcription / intracellular glucose homeostasis / positive regulation of glycolytic process / nuclear receptor binding / transcription corepressor binding / response to reactive oxygen species / RNA polymerase II transcription regulatory region sequence-specific DNA binding / euchromatin / ferrous iron binding / Hsp90 protein binding / cellular response to virus / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / RNA polymerase II transcription regulator complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / transcription coactivator binding / histone deacetylase binding / positive regulation of angiogenesis / p53 binding / transcription corepressor activity / regulation of gene expression / Neddylation / cellular response to oxidative stress / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / nuclear body / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of gene expression / protein domain specific binding / positive regulation of gene expression / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Hypoxia-inducible factor-1 alpha / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Cupin-like domain 8 / Cupin-like domain ...Hypoxia-inducible factor-1 alpha / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Cupin-like domain 8 / Cupin-like domain / PAS fold-3 / PAS fold / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Hypoxia-inducible factor 1-alpha / Hypoxia-inducible factor 1-alpha inhibitor / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsElkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Schlemminger, I. / Seibel, J.F. / Schofield, C.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1Alpha
Authors: Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C. / Ratcliffe, P. / Schofield, C.J.
History
DepositionAug 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / citation_author / Item: _citation.page_last / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FACTOR INHIBITING HIF1
S: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2296
Polymers44,8352
Non-polymers3944
Water2,504139
1
A: FACTOR INHIBITING HIF1
S: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules

A: FACTOR INHIBITING HIF1
S: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45912
Polymers89,6704
Non-polymers7888
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10420 Å2
ΔGint-135.59 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.264, 86.264, 147.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE PROTEIN IS A DIMERIC FORMED BY CHAIN A.A HETERODIMERIC ASSOCIATION OF CHAIN A WITH CHAIN SPRODUCES A TETRAMER.THE BURIED SURFACE AREA SHOWN BELOW IS AN AVERAGECALCULATED FOR THE HETEROTETRAMER AND DOES NOTCORRESPOND TO THE BURIED SURFACE AREA FOR THEHOMODIMER OF CHAIN A

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AS

#1: Protein FACTOR INHIBITING HIF1


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q969Q7, UniProt: Q9NWT6*PLUS
#2: Protein/peptide HYPOXIA-INDUCIBLE FACTOR 1 ALPHA / HIF-1 ALPHA / ARNT INTERACTING PROTEIN / MEMBER OF PAS PROTEIN 1


Mass: 4506.937 Da / Num. of mol.: 1
Fragment: C-TERMINAL TRANSACTIVATION DOMAIN FRAGMENT, RESIDUES 786-826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-GP-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16665

-
Non-polymers , 4 types, 143 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5
Details: 1.2M AMMONIUM SULPHATE, 4% PEG400, 0.1M HEPES PH7.5, ARGON ATMOSPHERE, 11MG/ML PROTEIN WITH 1MM FE(II), 2.5MM AKG AND 2.5MM PEPTIDE, pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
11.2 Mammonium sulfate1reservoir
24 %PEG4001reservoir
30.1 MHEPES1reservoirpH7.5
411 mg/mlFIH1drop
51 mMFe2+1drop
62 mM2OG/NOG1drop
71 mMCAD fragment1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.983
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.25→38.63 Å / Num. obs: 27294 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.444 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2104 7.7 %RANDOM
Rwork0.183 ---
obs0.185 25127 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 21 139 3023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212961
X-RAY DIFFRACTIONr_bond_other_d0.0010.022554
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9494026
X-RAY DIFFRACTIONr_angle_other_deg0.72735966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0373350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18915515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
X-RAY DIFFRACTIONr_nbd_refined0.2210.3693
X-RAY DIFFRACTIONr_nbd_other0.2040.32483
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.363
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6491.51767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22722847
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88731194
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1114.51179
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 170
Rwork0.194 1783
Refinement TLS params.Method: refined / Origin x: 22.224 Å / Origin y: 27.623 Å / Origin z: 28.583 Å
111213212223313233
T0.1744 Å2-0.0059 Å2-0.0546 Å2-0.0216 Å20.0427 Å2--0.0949 Å2
L1.1183 °20.7934 °20.5409 °2-2.4664 °21.2249 °2--1.3415 °2
S0.0358 Å °-0.1772 Å °-0.0521 Å °0.1763 Å °0.0025 Å °0.1089 Å °0.2114 Å °-0.0339 Å °-0.0383 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 349
2X-RAY DIFFRACTION1S795 - 822
Refinement
*PLUS
Rfactor Rfree: 0.217 / Rfactor Rwork: 0.183
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