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- EMDB-55309: Human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2 bound... -

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Basic information

Entry
Database: EMDB / ID: EMD-55309
TitleHuman ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2 bound to coenzyme A
Map data
Sample
  • Complex: Tetramer of heterodimers of SUCLG1-SUCLA2 bound to coenzyme A
    • Protein or peptide: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
    • Protein or peptide: Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial
  • Ligand: COENZYME A
KeywordsSuccinate / Complex / ATP / ADP / Coenzyme A / TRANSFERASE
Function / homology
Function and homology information


succinyl-CoA pathway / succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA catabolic process / succinyl-CoA metabolic process ...succinyl-CoA pathway / succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA catabolic process / succinyl-CoA metabolic process / succinate metabolic 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 / 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 ...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 / 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 domain superfamily
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBailey HJ / McCorvie TJ / Shrestha L / Rembeza E / Strain-Damerell C / Burgess-Brown N / Yue WW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2 bound to coenzyme A
Authors: Bailey HJ / McCorvie TJ / Yue WW
History
DepositionOct 7, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55309.png

Downloads & links

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Map

FileDownload / File: emd_55309.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.49038672 - 0.695265
Average (Standard dev.)0.00027187206 (±0.016000982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55309_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55309_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55309_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetramer of heterodimers of SUCLG1-SUCLA2 bound to coenzyme A

EntireName: Tetramer of heterodimers of SUCLG1-SUCLA2 bound to coenzyme A
Components
  • Complex: Tetramer of heterodimers of SUCLG1-SUCLA2 bound to coenzyme A
    • Protein or peptide: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
    • Protein or peptide: Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial
  • Ligand: COENZYME A

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Supramolecule #1: Tetramer of heterodimers of SUCLG1-SUCLA2 bound to coenzyme A

SupramoleculeName: Tetramer of heterodimers of SUCLG1-SUCLA2 bound to coenzyme A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 313 KDa

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Macromolecule #1: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial

MacromoleculeName: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: succinate-CoA ligase (GDP-forming)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.161875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SYTASRQHLY VDKNTKIICQ GFTGKQGTFH SQQALEYGTK LVGGTTPGKG GQTHLGLPVF NTVKEAKEQT GATASVIYVP PPFAAAAIN EAIEAEIPLV VCITEGIPQQ DMVRVKHKLL RQEKTRLIGP NCPGVINPGE CKIGIMPGHI HKKGRIGIVS R SGTLTYEA ...String:
SYTASRQHLY VDKNTKIICQ GFTGKQGTFH SQQALEYGTK LVGGTTPGKG GQTHLGLPVF NTVKEAKEQT GATASVIYVP PPFAAAAIN EAIEAEIPLV VCITEGIPQQ DMVRVKHKLL RQEKTRLIGP NCPGVINPGE CKIGIMPGHI HKKGRIGIVS R SGTLTYEA VHQTTQVGLG QSLCVGIGGD PFNGTDFIDC LEIFLNDSAT EGIILIGEIG GNAEENAAEF LKQHNSGPNS KP VVSFIAG LTAPPGRRMG HAGAIIAGGK GGAKEKISAL QSAGVVVSMS PAQLGTTIYK EFEKRKML

UniProtKB: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial

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Macromolecule #2: Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial

MacromoleculeName: Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: succinate-CoA ligase (ADP-forming)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.757012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSSG VDLGTENLYF QSMNLSLHEY MSMELLQEAG VSVPKGYVAK SPDEAYAIAK KLGSKDVVIK AQVLAGGRGK GTFESGLKG GVKIVFSPEE AKAVSSQMIG KKLFTKQTGE KGRICNQVLV CERKYPRREY YFAITMERSF QGPVLIGSSH G GVNIEDVA ...String:
MHHHHHHSSG VDLGTENLYF QSMNLSLHEY MSMELLQEAG VSVPKGYVAK SPDEAYAIAK KLGSKDVVIK AQVLAGGRGK GTFESGLKG GVKIVFSPEE AKAVSSQMIG KKLFTKQTGE KGRICNQVLV CERKYPRREY YFAITMERSF QGPVLIGSSH G GVNIEDVA AESPEAIIKE PIDIEEGIKK EQALQLAQKM GFPPNIVESA AENMVKLYSL FLKYDATMIE INPMVEDSDG AV LCMDAKI NFDSNSAYRQ KKIFDLQDWT QEDERDKDAA KANLNYIGLD GNIGCLVNGA GLAMATMDII KLHGGTPANF LDV GGGATV HQVTEAFKLI TSDKKVLAIL VNIFGGIMRC DVIAQGIVMA VKDLEIKIPV VVRLQGTRVD DAKALIADSG LKIL ACDDL DEAARMVVKL SEIVTLAKQA HVDVKFQLPI WQ

UniProtKB: Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial

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Macromolecule #3: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 3 / Number of copies: 4 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Component:
ConcentrationName
25.0 mMHEPES
150.0 mMNaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4100 / Average exposure time: 4.0 sec. / Average electron dose: 52.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 320000
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6g4q

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44786
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

6g4q


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitially flexible fitting used the Namdinator server
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9swj:
Human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2 bound to coenzyme A

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