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- PDB-6odd: Crystal structure of the human complex ACP-ISD11 -

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Basic information

Entry
Database: PDB / ID: 6odd
TitleCrystal structure of the human complex ACP-ISD11
Components
  • Acyl carrier protein, mitochondrial
  • LYR motif-containing protein 4
KeywordsBIOSYNTHETIC PROTEIN / Iron Sulfur Clusters / Cysteine desulfurase activity regulator
Function / homology
Function and homology information


[4Fe-4S] cluster assembly / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial iron-sulfur cluster assembly complex / Complex I biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding ...[4Fe-4S] cluster assembly / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial iron-sulfur cluster assembly complex / Complex I biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / acyl binding / iron-sulfur cluster assembly / acyl carrier activity / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / aerobic respiration / fatty acid binding / mitochondrial membrane / fatty acid biosynthetic process / mitochondrial inner membrane / nuclear body / mitochondrial matrix / calcium ion binding / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
LYRM4, LYR domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-8Q1 / Acyl carrier protein, mitochondrial / LYR motif-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHerrera, M.G. / Noguera, M.E. / Klinke, S. / Santos, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Friedreichs Ataxia Research Alliance (FARA) United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure of the Human ACP-ISD11 Heterodimer.
Authors: Herrera, M.G. / Noguera, M.E. / Sewell, K.E. / Agudelo Suarez, W.A. / Capece, L. / Klinke, S. / Santos, J.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: 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 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl carrier protein, mitochondrial
B: LYR motif-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2594
Polymers18,6782
Non-polymers5812
Water52229
1
A: Acyl carrier protein, mitochondrial
B: LYR motif-containing protein 4
hetero molecules

A: Acyl carrier protein, mitochondrial
B: LYR motif-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5188
Polymers37,3574
Non-polymers1,1614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area5250 Å2
ΔGint-46 kcal/mol
Surface area19000 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-5 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.190, 123.190, 123.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#1: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9845.247 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDUFAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14561
#2: Protein LYR motif-containing protein 4


Mass: 8833.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD34
#3: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.17 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The drop was a 1:1 mix of protein (in 10 mM Tris buffer, 25 mM NaCl, pH 7.5) and reservoir solution (0.1 M Tris pH 9.1, 0.1 M CaCl2, 23% tert-butanol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2→43.553 Å / Num. obs: 21240 / % possible obs: 99.7 % / Redundancy: 39.695 % / Biso Wilson estimate: 53.192 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.078 / Χ2: 1.227 / Net I/σ(I): 32.54 / Num. measured all: 843114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.1239.3821.8041.5333390.691.82798.3
2.12-2.2639.4120.9833.6732260.9240.996100
2.26-2.4441.5150.4858.8929690.9860.491100
2.44-2.6839.9760.2616.627580.9950.264100
2.68-2.9942.8190.14131.725060.9990.142100
2.99-3.4540.4710.07856.73220210.079100
3.45-4.2235.4450.05382.8189310.053100
4.22-5.9436.3940.04596.84147910.045100
5.94-43.55338.7320.033112.5186810.03499.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WGB

5wgb


Resolution: 2→43.553 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1061 5 %random selection
Rwork0.1925 ---
obs0.1937 21226 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 230.4 Å2 / Biso mean: 66.6292 Å2 / Biso min: 40.57 Å2
Refinement stepCycle: final / Resolution: 2→43.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 78 29 1417
Biso mean--67.17 56.03 -
Num. residues----159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9958-2.08660.34311280.3032457258598
2.0866-2.19660.28061320.244225022634100
2.1966-2.33420.25691320.222325022634100
2.3342-2.51440.23361320.200825042636100
2.5144-2.76740.25711320.216525142646100
2.7674-3.16780.23481330.219725242657100
3.1678-3.99070.20241340.184525412675100
3.9907-43.56460.19041380.168826212759100
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)
12.7794-0.5304-1.18723.75461.55414.28370.0714-0.0359-0.16940.1181-0.12780.0887-0.2237-0.43850.01850.4490.0603-0.05820.49260.06060.481317.698560.718314.3802
25.0686-0.91681.682.2922-0.01443.67330.08970.0717-0.44980.1270.0148-0.22410.13480.25-0.11050.39320.0307-0.08190.38170.05580.530638.439251.435811.3056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 89)
2X-RAY DIFFRACTION2(chain 'B' and resid 18 through 91)

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