[English] 日本語
Yorodumi
- PDB-6dv2: Crystal Structure of Human Mitochondrial Trifunctional Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dv2
TitleCrystal Structure of Human Mitochondrial Trifunctional Protein
Components
  • Trifunctional enzyme subunit alpha, mitochondrial
  • Trifunctional enzyme subunit beta, mitochondrial
KeywordsTRANSFERASE/OXIDOREDUCTASE / FATTY ACID BETA-OXIDATION / TRANSFERASE / TRANSFERASE-OXIDOREDUCTASE complex
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase / Beta oxidation of myristoyl-CoA to lauroyl-CoA / cardiolipin acyl-chain remodeling / Acyl chain remodeling of CL / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / mitochondrial fatty acid beta-oxidation multienzyme complex / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / 3-hydroxyacyl-CoA dehydratase activity ...long-chain-3-hydroxyacyl-CoA dehydrogenase / Beta oxidation of myristoyl-CoA to lauroyl-CoA / cardiolipin acyl-chain remodeling / Acyl chain remodeling of CL / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / mitochondrial fatty acid beta-oxidation multienzyme complex / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / 3-hydroxyacyl-CoA dehydratase activity / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase / acetyl-CoA C-acetyltransferase activity / 3-hydroxyacyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / enoyl-CoA hydratase activity / mitochondrial envelope / lncRNA binding / fatty acid beta-oxidation / mitochondrial nucleoid / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to insulin / gene expression / mitochondrial inner membrane / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to xenobiotic stimulus / protein-containing complex binding / endoplasmic reticulum / mitochondrion / RNA binding
Similarity search - Function
Fatty acid oxidation complex, alpha subunit, mitochondrial / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site ...Fatty acid oxidation complex, alpha subunit, mitochondrial / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trifunctional enzyme subunit alpha, mitochondrial / Trifunctional enzyme subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFu, Z. / Xia, C. / Battaile, K.P. / Kim, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)GM29076 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Crystal structure of human mitochondrial trifunctional protein, a fatty acid beta-oxidation metabolon.
Authors: Xia, C. / Fu, Z. / Battaile, K.P. / Kim, J.P.
History
DepositionJun 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trifunctional enzyme subunit beta, mitochondrial
B: Trifunctional enzyme subunit beta, mitochondrial
C: Trifunctional enzyme subunit beta, mitochondrial
D: Trifunctional enzyme subunit beta, mitochondrial
E: Trifunctional enzyme subunit beta, mitochondrial
F: Trifunctional enzyme subunit beta, mitochondrial
G: Trifunctional enzyme subunit alpha, mitochondrial
H: Trifunctional enzyme subunit alpha, mitochondrial
I: Trifunctional enzyme subunit alpha, mitochondrial
J: Trifunctional enzyme subunit alpha, mitochondrial
K: Trifunctional enzyme subunit alpha, mitochondrial
L: Trifunctional enzyme subunit alpha, mitochondrial


Theoretical massNumber of molelcules
Total (without water)770,83012
Polymers770,83012
Non-polymers00
Water0
1
A: Trifunctional enzyme subunit beta, mitochondrial
B: Trifunctional enzyme subunit beta, mitochondrial
G: Trifunctional enzyme subunit alpha, mitochondrial
H: Trifunctional enzyme subunit alpha, mitochondrial


Theoretical massNumber of molelcules
Total (without water)256,9434
Polymers256,9434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-47 kcal/mol
Surface area91690 Å2
MethodPISA
2
C: Trifunctional enzyme subunit beta, mitochondrial
D: Trifunctional enzyme subunit beta, mitochondrial
I: Trifunctional enzyme subunit alpha, mitochondrial
J: Trifunctional enzyme subunit alpha, mitochondrial


Theoretical massNumber of molelcules
Total (without water)256,9434
Polymers256,9434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-43 kcal/mol
Surface area90500 Å2
MethodPISA
3
E: Trifunctional enzyme subunit beta, mitochondrial
F: Trifunctional enzyme subunit beta, mitochondrial
K: Trifunctional enzyme subunit alpha, mitochondrial
L: Trifunctional enzyme subunit alpha, mitochondrial


Theoretical massNumber of molelcules
Total (without water)256,9434
Polymers256,9434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-44 kcal/mol
Surface area90520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.536, 237.938, 141.319
Angle α, β, γ (deg.)90.00, 105.610, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Trifunctional enzyme subunit beta, mitochondrial / TP-beta


Mass: 49354.793 Da / Num. of mol.: 6 / Fragment: residues 34-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADHB, MSTP029 / Plasmid: hTFPb_pET28 / Details (production host): plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55084, acetyl-CoA C-acyltransferase
#2: Protein
Trifunctional enzyme subunit alpha, mitochondrial / 78 kDa gastrin-binding protein / TP-alpha


Mass: 79116.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADHA, HADH / Plasmid: hTFPa_pET21 / Details (production host): plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P40939, enoyl-CoA hydratase, long-chain-3-hydroxyacyl-CoA dehydrogenase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 7 / Details: 0.1 M Heps pH 7.0, 12% pEG3350 and 0.2 M MgCl2 / PH range: 6.5-7.0

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→89.574 Å / Num. all: 100350 / Num. obs: 100350 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.132 / Rsym value: 0.105 / Net I/av σ(I): 7 / Net I/σ(I): 13.2 / Num. measured all: 530931
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.6-3.795.20.7281.1146240.3940.910.728100
3.79-4.025.20.481.6138520.2610.6030.4899.9
4.02-4.35.50.2822.7130110.1470.3480.282100
4.3-4.655.40.1764.4120850.0920.2170.176100
4.65-5.095.30.1435.4111560.0770.1780.143100
5.09-5.695.10.1216.4100940.0670.1530.121100
5.69-6.575.30.0958.288880.0520.120.095100
6.57-8.055.40.04516.675700.0240.0570.045100
8.05-11.3850.02328.858340.0130.030.02399.8
11.38-89.5745.20.01733.532360.010.0230.01799.3

-
Processing

Software
NameVersionClassification
CNS1.3refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AFW, 2WTB,

1afw

2wtb


Resolution: 3.6→89.56 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 7328872.17 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4955 5 %RANDOM
Rwork0.244 ---
obs0.244 99045 98.7 %-
Solvent computationBsol: 88.2372 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 122.6 Å2
Baniso -1Baniso -2Baniso -3
1--24.41 Å2-0 Å2-7.74 Å2
2--11.29 Å2-0 Å2
3---13.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1.04 Å0.82 Å
Refinement stepCycle: 1 / Resolution: 3.6→89.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52059 0 0 0 52059
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.581.5
X-RAY DIFFRACTIONc_mcangle_it13.622
X-RAY DIFFRACTIONc_scbond_it172
X-RAY DIFFRACTIONc_scangle_it22.952.5
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 782 4.8 %
Rwork0.343 15680 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top
X-RAY DIFFRACTION6CNS_TOPPAR/~/CNS13/cpr/cofac_human.par~/CNS13/cpr/cofac_human.top

+
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