[English] 日本語
Yorodumi
- PDB-8q6e: Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q6e
TitleAerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with Fe(III), 2-oxoglutarate (2OG) and HIF2alpha-CODD peptide
Components
  • Egl nine homolog 1
  • Endothelial PAS domain-containing protein 1
KeywordsOXIDOREDUCTASE / 2OG oxygenases / oxygen sensor / jelly-roll
Function / homology
Function and homology information


myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells ...myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / intracellular oxygen homeostasis / labyrinthine layer development / norepinephrine metabolic process / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / heart trabecula formation / regulation of modification of postsynaptic structure / surfactant homeostasis / L-ascorbic acid binding / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / embryonic placenta development / response to nitric oxide / ventricular septum morphogenesis / blood vessel remodeling / regulation of angiogenesis / visual perception / Pexophagy / regulation of heart rate / erythrocyte differentiation / lung development / mitochondrion organization / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / cellular response to hypoxia / Neddylation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / angiogenesis / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / intracellular membrane-bounded organelle / glutamatergic synapse / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. ...: / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Endothelial PAS domain-containing protein 1 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsFiorini, G. / Figg Jr, W.D. / Schofield, C.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
University of Oxford, Medical Sciences Internal Fund (MSIF) United Kingdom
Cancer Research UK United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: HIF prolyl hydroxylase 2 in complex with HIF2alpha-CODD
Authors: Fiorini, G. / Figg Jr, W.D. / Schofield, C.J.
History
DepositionAug 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Egl nine homolog 1
B: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6929
Polymers28,3462
Non-polymers3467
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-69 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.900, 38.120, 42.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

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

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing ...Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 26036.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Protein/peptide Endothelial PAS domain-containing protein 1 / EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / ...EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / bHLHe73 / HIF-1-alpha-like factor / HLF / Hypoxia-inducible factor 2-alpha / HIF-2-alpha / HIF2-alpha / Member of PAS protein 2 / PAS domain-containing protein 2


Mass: 2309.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPAS1, BHLHE73, HIF2A, MOP2, PASD2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q99814

-
Non-polymers , 5 types, 253 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: (10-35%) PEG 4K, 0.2 M ammonium acetate , 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.3→43.61 Å / Num. obs: 52821 / % possible obs: 98.5 % / Redundancy: 11.6 % / CC1/2: 1 / Net I/σ(I): 12.7
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 2130 / CC1/2: 0.3

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→42.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2299 5.01 %
Rwork0.1797 --
obs0.181 45878 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 16 246 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131961
X-RAY DIFFRACTIONf_angle_d1.2562674
X-RAY DIFFRACTIONf_dihedral_angle_d6.516286
X-RAY DIFFRACTIONf_chiral_restr0.094285
X-RAY DIFFRACTIONf_plane_restr0.016357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.46581610.43152583X-RAY DIFFRACTION97
1.4-1.430.36861610.37612656X-RAY DIFFRACTION100
1.43-1.470.34021460.31032697X-RAY DIFFRACTION100
1.47-1.510.27491180.272691X-RAY DIFFRACTION100
1.51-1.550.29811570.25252668X-RAY DIFFRACTION100
1.55-1.60.28111410.22942686X-RAY DIFFRACTION100
1.6-1.660.24791390.21352726X-RAY DIFFRACTION100
1.66-1.730.23911380.18962701X-RAY DIFFRACTION100
1.73-1.80.21011380.17012700X-RAY DIFFRACTION100
1.8-1.90.19351340.16262735X-RAY DIFFRACTION100
1.9-2.020.211400.15982720X-RAY DIFFRACTION100
2.02-2.170.18541360.15352734X-RAY DIFFRACTION100
2.17-2.390.181390.1552778X-RAY DIFFRACTION100
2.39-2.740.19271450.16982764X-RAY DIFFRACTION100
2.74-3.450.16451630.16662770X-RAY DIFFRACTION100
3.45-42.770.19471430.16652970X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.863-0.4590.66882.0862-0.74483.4112-0.123-0.07320.21610.09990.0382-0.0422-0.2104-0.21010.07940.20710.0166-0.02670.1695-0.03630.267714.572424.65811.9505
21.3316-0.3163-0.26266.46023.22512.7411-0.0212-0.21270.05180.7870.0908-0.5775-0.0535-0.0127-0.07940.3830.0303-0.08380.28380.0360.264418.6736.534227.1875
31.6375-0.61990.21311.755-0.23831.1399-0.0242-0.0928-0.11850.11430.0372-0.04170.0544-0.0504-0.00530.1560.0007-0.02950.1393-0.00050.204314.32725.338611.6165
42.30640.0240.85371.3850.10062.09820.0259-0.0334-0.0530.0786-0.0127-0.2503-0.03270.1083-0.010.16210.002-0.03040.11860.00220.229624.64199.557810.5279
51.43780.0681-0.16331.19150.3451.7162-0.04550.0270.2399-0.02190.0306-0.1873-0.11990.1220.0050.19230.0089-0.03310.1534-0.00760.287924.706317.72347.7615
66.012-2.47024.99983.7961-4.31488.22080.05970.01170.1344-0.1005-0.0803-0.43050.11820.14590.01290.12980.01-0.00890.0949-0.03930.240228.128810.46485.5491
74.74081.01854.31621.28411.07135.4604-0.08990.1163-0.0146-0.04550.0362-0.0241-0.0033-0.02340.05180.1509-0.0053-0.00090.15160.00010.191610.5915.54213.3097
88.93080.54583.8092.629-1.60252.9246-0.03490.7836-0.5856-1.06070.1132-0.52620.870.1563-0.02890.3208-0.00040.02740.2297-0.05520.307522.90891.6881-5.1453
94.6868-3.7527-5.26223.57333.77326.1893-0.1430.4644-0.61970.1307-0.20260.49070.3313-0.59370.28610.2448-0.01560.00550.23430.02050.35946.96322.79726.4307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 188 through 215 )
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 304 )
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 342 )
5X-RAY DIFFRACTION5chain 'A' and (resid 343 through 369 )
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 381 )
7X-RAY DIFFRACTION7chain 'A' and (resid 382 through 406 )
8X-RAY DIFFRACTION8chain 'B' and (resid 524 through 529 )
9X-RAY DIFFRACTION9chain 'B' and (resid 530 through 542 )

+
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://pdbjlc1.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