[English] 日本語
Yorodumi
- PDB-7a1k: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-((9,9-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a1k
TitleFACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-((9,9-dimethyl-9H-fluoren-2-yl)methyl)-2-oxoglutarate
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / Hypoxia-inducible factor asparagine hydroxylase / Dioxygenase
Function / homology
Function and homology information


hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding / oxygen sensor activity / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold
Similarity search - Domain/homology
Chem-QVZ / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2021
Title: 2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases.
Authors: Nakashima, Y. / Brewitz, L. / Tumber, A. / Salah, E. / Schofield, C.J.
History
DepositionAug 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 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: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1307
Polymers40,3281
Non-polymers8026
Water1,13563
1
A: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules

A: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,26114
Polymers80,6572
Non-polymers1,60412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4460 Å2
ΔGint-125 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.181, 86.181, 148.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Hypoxia-inducible factor 1-alpha inhibitor / Factor inhibiting HIF-1 / FIH-1 / Hypoxia-inducible factor asparagine hydroxylase


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QVZ / 3-((9,9-dimethyl-9H-fluoren-2-yl)methyl)-2-oxoglutarate / (3~{S})-3-[(9,9-dimethylfluoren-2-yl)methyl]-2-oxidanylidene-pentanedioic acid


Mass: 352.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.99→74.588 Å / Num. obs: 73389 / % possible obs: 100 % / Redundancy: 26.2 % / Biso Wilson estimate: 56.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 21.5
Reflection shellResolution: 1.99→2.024 Å / Redundancy: 27.7 % / Rmerge(I) obs: 5.665 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1927 / CC1/2: 0.38 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2K

1h2k


Resolution: 1.99→41.39 Å / SU ML: 0.3075 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 3628 4.94 %
Rwork0.2066 69761 -
obs0.2076 73389 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.9 Å2
Refinement stepCycle: LAST / Resolution: 1.99→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 0 63 2831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862882
X-RAY DIFFRACTIONf_angle_d0.67323937
X-RAY DIFFRACTIONf_chiral_restr0.0536396
X-RAY DIFFRACTIONf_plane_restr0.0049521
X-RAY DIFFRACTIONf_dihedral_angle_d17.5521057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.46381390.43032663X-RAY DIFFRACTION98.49
2.02-2.040.36511370.39772670X-RAY DIFFRACTION99.33
2.04-2.070.33931290.36042689X-RAY DIFFRACTION99.72
2.07-2.10.34091350.32472666X-RAY DIFFRACTION99.26
2.1-2.140.36891400.33132681X-RAY DIFFRACTION99.86
2.14-2.170.35931340.31432686X-RAY DIFFRACTION100
2.17-2.210.34891620.28212689X-RAY DIFFRACTION99.89
2.21-2.250.27231450.2592647X-RAY DIFFRACTION99.82
2.25-2.290.27311430.25322688X-RAY DIFFRACTION99.96
2.29-2.340.24961520.2382673X-RAY DIFFRACTION100
2.34-2.390.28071420.22372728X-RAY DIFFRACTION99.97
2.39-2.450.27111480.21062639X-RAY DIFFRACTION100
2.45-2.510.23971440.21632674X-RAY DIFFRACTION100
2.51-2.570.22541260.21312696X-RAY DIFFRACTION100
2.57-2.650.26311410.22582709X-RAY DIFFRACTION100
2.65-2.740.23181240.21962675X-RAY DIFFRACTION99.96
2.74-2.830.24211150.22412730X-RAY DIFFRACTION99.93
2.83-2.950.26611160.23752682X-RAY DIFFRACTION99.96
2.95-3.080.27521570.24252697X-RAY DIFFRACTION99.96
3.08-3.240.26821160.24762709X-RAY DIFFRACTION100
3.24-3.450.28551440.22252710X-RAY DIFFRACTION100
3.45-3.710.2291540.2032633X-RAY DIFFRACTION100
3.71-4.090.18981310.18112718X-RAY DIFFRACTION100
4.09-4.680.17931740.15072636X-RAY DIFFRACTION99.96
4.68-5.890.19091340.1722680X-RAY DIFFRACTION100
5.89-41.390.20931460.20952693X-RAY DIFFRACTION99.82
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)
11.475895080410.7849861135630.144708148810.847462500545-0.4635381495760.694946320575-0.2132304714210.282827763268-0.0974686720655-0.834750965109-0.3039202311531.13804602543-0.356335295432-0.4260243053830.4428333739320.934713557379-0.00169528252184-0.2705130495640.610256614063-0.03191095179591.0625698814710.535040273629.507301850314.3052444682
22.744779201880.111949462132-0.0137264280723.231766015521.729434964641.86344600528-0.0473209708786-0.490542802584-0.2396241736360.6861998775020.0113155359150.3058308775420.616439334318-0.1391687509610.02689571825690.850457245927-0.0244869247228-0.05295866857440.4946275998550.09249663673740.57569441627518.901616673318.151577528530.3023496824
31.026787243310.2145713294510.5422158184542.113703898670.8407020591082.21612591343-0.0170126166582-0.1020859256930.01706230496310.008734503015810.04520491842520.1794940309960.0104574551483-0.000604387612602-0.04730132812140.684160828177-0.0192970638723-0.1067899624310.4396526170050.0113796549980.60202254994324.426220011533.595840282727.6763474425
46.339418273632.00990691208-1.780301073966.13571291006-0.7103324509535.09176982796-0.184471890513-0.4046099653520.640316160284-0.04742003137250.1432971293850.5859420628270.3861349435310.07847274592-0.07795735014070.52828171678-0.0240683881463-0.06115481663370.684260628369-0.0897828478240.49489738986237.512612704749.880498293842.3160146336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 330 )
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 349 )

+
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