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- PDB-6g4q: Structure of human ADP-forming succinyl-CoA ligase complex SUCLG1... -

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Basic information

Entry
Database: PDB / ID: 6g4q
TitleStructure of human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2
Components
  • Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial
  • Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
KeywordsLIGASE / Complex / Succinyl-CoA Ligase / Mitochondrial / ATP-specific
Function / homology
Function and homology information


succinyl-CoA pathway / succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA catabolic process ...succinyl-CoA pathway / succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA catabolic process / Citric acid cycle (TCA cycle) / tricarboxylic acid cycle / mitochondrial matrix / nucleotide binding / magnesium ion binding / mitochondrion / RNA binding / extracellular exosome / ATP binding
Similarity search - Function
Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / 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. ...Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / 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 / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBailey, H.J. / Shrestha, L. / Rembeza, E. / Sorrell, F.J. / Newman, J. / Strain-Damerell, C. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. ...Bailey, H.J. / Shrestha, L. / Rembeza, E. / Sorrell, F.J. / Newman, J. / Strain-Damerell, C. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To Be Published
Title: Structure of human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2
Authors: Bailey, H.J. / Shrestha, L. / Rembeza, E. / Sorrell, F.J. / Strain-Damerell, C. / Burgess-Brown, N. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
B: Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,15410
Polymers77,6572
Non-polymers4978
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-2 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.200, 130.200, 119.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinyl-CoA synthetase subunit alpha / SCS-alpha


Mass: 32459.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG1 / Production host: Escherichia coli (E. coli)
References: UniProt: P53597, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming)
#2: Protein Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial / ATP-specific succinyl-CoA synthetase subunit beta / A-SCS / Succinyl-CoA synthetase beta-A chain / SCS-betaA


Mass: 45198.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLA2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P2R7, succinate-CoA ligase (ADP-forming)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.1M DL- malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.59→65.1 Å / Num. obs: 36946 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 2.59→2.66 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2712 / CC1/2: 0.547 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUC

1euc


Resolution: 2.59→65.1 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.31
RfactorNum. reflection% reflection
Rfree0.2535 1693 4.65 %
Rwork0.2075 --
obs0.2096 36407 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 187.17 Å2 / Biso mean: 78.9871 Å2 / Biso min: 37.29 Å2
Refinement stepCycle: final / Resolution: 2.59→65.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 32 82 5136
Biso mean--82.65 67.1 -
Num. residues----698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.589-2.66510.46281360.39432726286294
2.6651-2.75120.43841260.35892814294096
2.7512-2.84950.4011370.3252838297597
2.8495-2.96360.36491260.29842876300299
2.9636-3.09850.34771480.26362853300198
3.0985-3.26180.29011230.24622895301899
3.2618-3.46620.29271460.21232886303299
3.4662-3.73380.2461490.18929103059100
3.7338-4.10950.23621520.174429293081100
4.1095-4.7040.17511530.148429333086100
4.704-5.92590.20241530.189529743127100
5.9259-65.12060.24471440.195930803224100
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)
18.29350.5253-3.59143.0966-0.03583.7525-0.0826-0.099-0.8638-0.28810.1943-0.08910.9014-0.0024-0.12480.83410.0212-0.11070.33820.03820.4224-60.0874-17.020730.3693
25.35612.0551-1.24692.9361-1.45414.7661-0.0064-0.3241-0.2805-0.06470.25220.2870.6177-0.6601-0.2330.7106-0.0709-0.02990.41680.09930.4374-67.3549-9.593933.5097
32.1196-0.98670.42242.88630.19765.45410.07280.1159-0.4193-0.0933-0.00080.40060.5125-0.0731-0.18410.7101-0.0634-0.08480.3122-0.02270.4981-62.0468-15.610717.2162
43.3272-1.26350.23393.7281-0.04146.54070.20220.2547-0.24250.17970.0305-0.23260.52450.9629-0.22650.60980.0558-0.08370.509-0.11750.4107-49.3425-14.83514.6169
55.8958-4.00622.80137.4457-5.43945.88350.46370.40630.047-0.6668-0.38580.0083-0.40880.4869-0.11650.5954-0.15810.01420.4986-0.0830.3472-53.5536-4.63748.7835
62.9052-2.275-1.4734.7984-2.4844.96710.50.38310.1758-0.5113-0.1263-0.1544-0.09710.5705-0.3610.76110.0281-0.03270.6512-0.16370.4156-50.445-9.54822.5878
79.8185-3.47242.2133.6137-3.95864.80220.92310.0037-0.3908-0.6251-0.6057-0.71180.49270.4949-0.43681.05930.0853-0.20510.5709-0.20210.7006-54.1978-24.59320.8601
81.3690.7227-1.65056.2321-3.32872.62620.0330.45090.1701-0.02950.1259-0.1982-0.0616-0.2114-0.14770.6226-0.11520.03710.62360.03110.5138-49.23525.076517.029
91.25630.51881.36781.76891.233.24080.07940.01660.0224-0.0614-0.16870.1465-0.0539-0.49050.18660.64750.01780.03720.50630.01790.4929-70.08514.1093.7245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 65 )A41 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 161 )A66 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 235 )A162 - 235
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 273 )A236 - 273
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 310 )A274 - 310
6X-RAY DIFFRACTION6chain 'A' and (resid 311 through 331 )A311 - 331
7X-RAY DIFFRACTION7chain 'A' and (resid 332 through 345 )A332 - 345
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 249 )B53 - 249
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 463 )B250 - 463

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