[English] 日本語
Yorodumi
- PDB-36ad: Fumarate hydratase (human mitochondrial) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 36ad
TitleFumarate hydratase (human mitochondrial)
ComponentsFumarate hydratase, mitochondrial
KeywordsLYASE / human fumarate hydratase / L-tartrate complex
Function / homology
Function and homology information


: / fumarate hydratase activity / fumarate hydratase / Citric acid cycle (TCA cycle) / fumarate metabolic process / arginine metabolic process / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / tricarboxylic acid cycle ...: / fumarate hydratase activity / fumarate hydratase / Citric acid cycle (TCA cycle) / fumarate metabolic process / arginine metabolic process / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / tricarboxylic acid cycle / Mitochondrial protein degradation / homeostasis of number of cells within a tissue / positive regulation of cold-induced thermogenesis / chromosome / site of double-strand break / histone binding / mitochondrial matrix / DNA repair / DNA damage response / mitochondrion / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Fumarate hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsWeaver, T.M. / May, J.F. / Bhattacharyya, B. / Strauss, L.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Other government United States
Other private United States
CitationJournal: To Be Published
Title: Fumarate hydratase (human mitochondrial)
Authors: Weaver, T.M. / May, J.F. / Bhattacharyya, B. / Strauss, L.A.
History
DepositionMay 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
C: Fumarate hydratase, mitochondrial
D: Fumarate hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,9535
Polymers218,8034
Non-polymers1501
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28320 Å2
ΔGint-174 kcal/mol
Surface area54500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.490, 189.490, 115.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein
Fumarate hydratase, mitochondrial / Fumarase / HsFH


Mass: 54700.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal 6x his-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: FH / Plasmid: pMMB1922 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 derivative / References: UniProt: P07954, fumarate hydratase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium potassium tartrate 01. M Bis-Tris pH 6.5 10% PEG 10,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2025
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.11→73.37 Å / Num. obs: 137305 / % possible obs: 99.99 % / Redundancy: 21.2 % / Biso Wilson estimate: 44.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.209 / Net I/σ(I): 12.3
Reflection shellResolution: 2.11→2.15 Å / Rmerge(I) obs: 3.634 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6746 / CC1/2: 0.317

-
Processing

Software
NameVersionClassification
xia23.21.1data reduction
xia23.21.1data scaling
PHENIX1.20.1-4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→66.98 Å / SU ML: 0.2713 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 6912 5.04 %
Rwork0.1793 130317 -
obs0.1809 137229 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.09 Å2
Refinement stepCycle: LAST / Resolution: 2.11→66.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13561 0 10 485 14056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002113878
X-RAY DIFFRACTIONf_angle_d0.507818809
X-RAY DIFFRACTIONf_chiral_restr0.03872176
X-RAY DIFFRACTIONf_plane_restr0.00422452
X-RAY DIFFRACTIONf_dihedral_angle_d12.0825137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.130.37212530.35644260X-RAY DIFFRACTION99.58
2.13-2.160.35692520.32244252X-RAY DIFFRACTION99.76
2.16-2.190.34392490.3094307X-RAY DIFFRACTION100
2.19-2.210.26482110.27894290X-RAY DIFFRACTION99.8
2.21-2.240.30942070.2744342X-RAY DIFFRACTION99.87
2.24-2.270.29312650.25364279X-RAY DIFFRACTION99.87
2.27-2.310.27592200.24664319X-RAY DIFFRACTION99.89
2.31-2.340.25992420.2424340X-RAY DIFFRACTION99.96
2.34-2.380.28362460.23854263X-RAY DIFFRACTION99.96
2.38-2.420.26682190.23934391X-RAY DIFFRACTION100
2.42-2.460.2562540.23854285X-RAY DIFFRACTION99.96
2.46-2.50.28192080.23464306X-RAY DIFFRACTION100
2.5-2.550.26312450.20624298X-RAY DIFFRACTION99.96
2.55-2.60.2342170.20534334X-RAY DIFFRACTION100
2.6-2.660.2222280.18694347X-RAY DIFFRACTION100
2.66-2.720.21742520.18854337X-RAY DIFFRACTION100
2.72-2.790.24612100.17754329X-RAY DIFFRACTION100
2.79-2.860.22632370.1764320X-RAY DIFFRACTION100
2.86-2.950.24992290.18414380X-RAY DIFFRACTION100
2.95-3.040.23562270.19824342X-RAY DIFFRACTION100
3.04-3.150.22882310.1964328X-RAY DIFFRACTION100
3.15-3.280.21832160.18524361X-RAY DIFFRACTION100
3.28-3.430.21151970.17934380X-RAY DIFFRACTION100
3.43-3.610.19231930.16794410X-RAY DIFFRACTION100
3.61-3.830.19072360.16374354X-RAY DIFFRACTION100
3.83-4.130.17682330.14294389X-RAY DIFFRACTION100
4.13-4.550.13892430.13074357X-RAY DIFFRACTION100
4.55-5.20.16042220.13734429X-RAY DIFFRACTION100
5.2-6.550.21852500.17774432X-RAY DIFFRACTION100
6.56-66.980.19132200.16274556X-RAY DIFFRACTION99.42
Refinement TLS params.Method: refined / Origin x: -61.2118955525 Å / Origin y: -75.5009458912 Å / Origin z: -28.6567563087 Å
111213212223313233
T0.277331666088 Å20.0194678651053 Å2-0.0358952490534 Å2-0.306102658555 Å2-0.0386454594609 Å2--0.287476939751 Å2
L0.676469921534 °2-0.0667954567258 °2-0.0536955923752 °2-0.646630805822 °2-0.143935193613 °2--0.701157824043 °2
S0.0178286243007 Å °0.0467872642223 Å °-0.0221683096693 Å °-0.0449473090994 Å °0.00575381893234 Å °0.110110372079 Å °0.0218235472816 Å °-0.02270905184 Å °-0.0237614151138 Å °
Refinement TLS groupSelection details: all

+
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