[English] 日本語
Yorodumi
- PDB-3mwd: Truncated Human ATP-Citrate Lyase with Citrate Bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mwd
TitleTruncated Human ATP-Citrate Lyase with Citrate Bound
Components(ATP-citrate synthase) x 2
KeywordsTRANSFERASE / ATP-grasp / phosphohistidine / organic acid / LYASE
Function / homology
Function and homology information


ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol
Similarity search - Function
Succinyl-CoA synthetase domains / ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. ...Succinyl-CoA synthetase domains / ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsFraser, M.E. / Sun, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography.
Authors: Sun, T. / Hayakawa, K. / Bateman, K.S. / Fraser, M.E.
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4073
Polymers84,2152
Non-polymers1921
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules

A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8136
Polymers168,4294
Non-polymers3842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9020 Å2
ΔGint-40 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.197, 61.704, 109.421
Angle α, β, γ (deg.)90.00, 125.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / Citrate cleavage enzyme


Mass: 47323.152 Da / Num. of mol.: 1
Fragment: Truncated Human ATP-Citrate Lyase (UNP residues 1-425)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET42b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53396, ATP citrate synthase
#2: Protein ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / Citrate cleavage enzyme


Mass: 36891.441 Da / Num. of mol.: 1
Fragment: Truncated Human ATP-Citrate Lyase (UNP residues 487-820)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET42b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53396, ATP citrate synthase
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALS WERE GROWN WITH LIMITED PROTEOLYIS BY STARTING WILL FULL LENGTH PROTEIN AND EXPRESSION TAG. ...CRYSTALS WERE GROWN WITH LIMITED PROTEOLYIS BY STARTING WILL FULL LENGTH PROTEIN AND EXPRESSION TAG. BY SDS-PAGE ANALYSIS OF DISSOLVED CRYSTALS AND SUBSEQUENT MASS SPECTROMETRY TWO CRYSTALLIZED PORTIONS WERE IDENTIFIED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 294 K / pH: 7
Details: 10% (w/v) PEG 3350, 75 mM potassium citrate, 100 mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98055, 0.9808
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2008
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980551
20.98081
ReflectionResolution: 2.1→56.34 Å / Num. obs: 54277 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→44.82 Å / SU ML: 0.31 / σ(F): 0.75 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 6072 5.74 %
Rwork0.191 --
obs0.194 54277 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.46 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1539 Å20 Å23.0235 Å2
2--6.3309 Å2-0 Å2
3----4.177 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 0 13 359 6110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075896
X-RAY DIFFRACTIONf_angle_d1.0587991
X-RAY DIFFRACTIONf_dihedral_angle_d12.6862187
X-RAY DIFFRACTIONf_chiral_restr0.069895
X-RAY DIFFRACTIONf_plane_restr0.0041024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.34671890.3053360X-RAY DIFFRACTION100
2.1239-2.14880.29121740.273346X-RAY DIFFRACTION100
2.1488-2.17510.31471950.26283336X-RAY DIFFRACTION100
2.1751-2.20260.30251750.27193377X-RAY DIFFRACTION100
2.2026-2.23160.2961740.26323301X-RAY DIFFRACTION100
2.2316-2.26210.29711690.24813350X-RAY DIFFRACTION100
2.2621-2.29450.29331890.24183354X-RAY DIFFRACTION100
2.2945-2.32870.28851860.23853324X-RAY DIFFRACTION100
2.3287-2.36510.28081550.23373446X-RAY DIFFRACTION100
2.3651-2.40390.27891790.23033212X-RAY DIFFRACTION100
2.4039-2.44530.25741890.21923418X-RAY DIFFRACTION100
2.4453-2.48980.25651590.21743393X-RAY DIFFRACTION100
2.4898-2.53770.26841990.21853273X-RAY DIFFRACTION100
2.5377-2.58940.27472280.2173287X-RAY DIFFRACTION100
2.5894-2.64570.2622280.21543309X-RAY DIFFRACTION100
2.6457-2.70730.25032160.21313291X-RAY DIFFRACTION100
2.7073-2.7750.24582200.21833351X-RAY DIFFRACTION100
2.775-2.850.26442270.2143288X-RAY DIFFRACTION100
2.85-2.93380.27392040.21193314X-RAY DIFFRACTION100
2.9338-3.02850.25642290.20663303X-RAY DIFFRACTION100
3.0285-3.13670.21432150.19853315X-RAY DIFFRACTION100
3.1367-3.26230.22992190.19263300X-RAY DIFFRACTION100
3.2623-3.41070.19732230.173315X-RAY DIFFRACTION100
3.4107-3.59050.20492260.16853322X-RAY DIFFRACTION100
3.5905-3.81530.18052160.15243275X-RAY DIFFRACTION100
3.8153-4.10970.17132170.1493325X-RAY DIFFRACTION100
4.1097-4.52290.17892120.13613291X-RAY DIFFRACTION100
4.5229-5.17660.15712260.13373321X-RAY DIFFRACTION100
5.1766-6.51870.22532190.15523301X-RAY DIFFRACTION100
6.5187-44.82910.20282150.16913311X-RAY DIFFRACTION100

+
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://pdbjlvh1.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