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- PDB-5wlw: Crystal Structure of the Human Mitochondrial Cysteine Desulfurase... -

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Basic information

Entry
Database: PDB / ID: 5wlw
TitleCrystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A.
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / Human mitochondrial cysteine desulfurse LYR Motif containing protein 4 Iron-Sulfur Cluster Scaffold Protein ISCU1 with Zn in the active site Acyl Carrier Protein 1 (E.coli)
Function / homology
Function and homology information


negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / positive regulation of aconitate hydratase activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone ...negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / positive regulation of aconitate hydratase activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / lipid A biosynthetic process / iron-sulfur cluster binding / acyl binding / acyl carrier activity / ferrous iron binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / Maturation of replicase proteins / intracellular iron ion homeostasis / molecular adaptor activity / nuclear body / mitochondrial matrix / iron ion binding / centrosome / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
LYRM4, LYR domain / ISC system FeS cluster assembly, IscU scaffold / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. ...LYRM4, LYR domain / ISC system FeS cluster assembly, IscU scaffold / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / Iron-sulfur cluster assembly enzyme ISCU / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.317 Å
AuthorsBoniecki, M.T. / Cygler, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.
Authors: Boniecki, M.T. / Freibert, S.A. / Muhlenhoff, U. / Lill, R. / Cygler, M.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase, mitochondrial
B: LYR motif-containing protein 4
C: Acyl carrier protein
D: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
E: Cysteine desulfurase, mitochondrial
F: LYR motif-containing protein 4
G: Acyl carrier protein
H: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,10114
Polymers161,3948
Non-polymers1,7066
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19340 Å2
ΔGint-207 kcal/mol
Surface area51220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.529, 121.241, 151.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Cysteine desulfurase, mitochondrial


Mass: 45081.578 Da / Num. of mol.: 2 / Fragment: UNP residues 56-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y697, cysteine desulfurase
#2: Protein LYR motif-containing protein 4


Mass: 10763.483 Da / Num. of mol.: 2
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: Protein Acyl carrier protein / ACP


Mass: 8514.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: acpP, ECS88_1108 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MJ81
#4: Protein Iron-sulfur cluster assembly enzyme ISCU, mitochondrial / NifU-like N-terminal domain-containing protein / NifU-like protein


Mass: 16337.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU, NIFUN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1K1

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Non-polymers , 3 types, 6 molecules

#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: 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.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 7.0 15 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.3→48.85 Å / Num. obs: 27282 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 0.997 / Net I/σ(I): 13.7
Reflection shellResolution: 3.3→3.52 Å / Mean I/σ(I) obs: 2.73 / CC1/2: 0.87 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMV, 3LVL, 2FAE

3lmv

3lvl

2fae


Resolution: 3.317→48.764 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2000 7.35 %
Rwork0.1962 --
obs0.2005 27205 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.317→48.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9863 0 2 0 9865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210025
X-RAY DIFFRACTIONf_angle_d0.57913646
X-RAY DIFFRACTIONf_dihedral_angle_d14.1326035
X-RAY DIFFRACTIONf_chiral_restr0.0411632
X-RAY DIFFRACTIONf_plane_restr0.0041760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3172-3.40020.34461390.29651747X-RAY DIFFRACTION98
3.4002-3.49210.37261400.26831767X-RAY DIFFRACTION100
3.4921-3.59480.29341400.24171769X-RAY DIFFRACTION100
3.5948-3.71080.28251410.21551772X-RAY DIFFRACTION100
3.7108-3.84340.26371400.19541763X-RAY DIFFRACTION100
3.8434-3.99720.2611430.18881792X-RAY DIFFRACTION100
3.9972-4.1790.25031420.18531789X-RAY DIFFRACTION100
4.179-4.39920.27451400.18631784X-RAY DIFFRACTION100
4.3992-4.67460.22561440.17191802X-RAY DIFFRACTION100
4.6746-5.03520.24981430.16511809X-RAY DIFFRACTION100
5.0352-5.54130.2291430.18691799X-RAY DIFFRACTION100
5.5413-6.34160.25921440.20471821X-RAY DIFFRACTION100
6.3416-7.98410.22481470.19761855X-RAY DIFFRACTION100
7.9841-48.76970.22711540.17941936X-RAY DIFFRACTION100
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)
11.82260.1357-0.1171.11550.23631.8862-0.0158-0.0487-0.075-0.1543-0.07020.06730.1402-0.11920.03960.47220.0250.04220.46090.01970.4845.355235.724856.3717
20.83590.51470.61192.531-0.18292.1625-0.0465-0.20730.0198-0.13770.1709-0.30260.4834-0.4633-0.12240.6263-0.00060.13130.61840.04760.705543.978319.42681.0217
31.0765-0.2785-0.21620.69770.01350.53640.0254-0.4848-0.39490.12220.2385-0.22150.5122-0.0479-0.01631.003-0.07960.05120.53640.17870.992239.09210.193285.9497
40.3689-0.3729-0.09930.9677-0.24180.7913-0.18290.1168-0.3333-0.04390.27540.49150.2024-0.3654-0.03130.8597-0.1311-0.1451.59840.07141.20228.078331.757340.0754
50.81090.24870.05731.47240.24041.1868-0.0946-0.1410.14020.01150.0807-0.0352-0.1564-0.1236-0.00150.49120.04910.01770.6312-0.04230.540441.929864.024676.6022
60.76530.2873-0.13411.27680.40391.05620.4042-0.52410.4099-0.0681-0.26450.2359-0.019-0.2125-0.05570.53760.03420.12230.901-0.03290.675426.97346.598295.6958
71.21620.31010.13450.9583-0.19131.34190.34180.1723-0.31990.34-0.02080.0687-0.3485-0.231-0.35410.74940.0523-0.0231.125-0.12010.740424.08746.7202115.5
81.9117-0.7167-0.16071.5581-0.28671.0987-0.05630.6006-0.4077-0.04580.041-0.03420.1218-0.0351-0.14860.73590.0142-0.09440.8005-0.1430.649279.659269.406195.1644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 54:452 OR RESID 501:501 ) )A54 - 452
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 54:452 OR RESID 501:501 ) )A501
3X-RAY DIFFRACTION2( CHAIN B AND RESID 5:85 )B5 - 85
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 4:74 OR RESID 301:301 ) )C4 - 74
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 4:74 OR RESID 301:301 ) )C301
6X-RAY DIFFRACTION4( CHAIN D AND RESID 6:133 )D6 - 133
7X-RAY DIFFRACTION5( CHAIN E AND ( RESID 54:454 OR RESID 501:501 ) )E54 - 454
8X-RAY DIFFRACTION5( CHAIN E AND ( RESID 54:454 OR RESID 501:501 ) )E501
9X-RAY DIFFRACTION6( CHAIN F AND RESID 3:85 )F3 - 85
10X-RAY DIFFRACTION7( CHAIN G AND ( RESID 3:72 OR RESID 301:301 ) )G3 - 72
11X-RAY DIFFRACTION7( CHAIN G AND ( RESID 3:72 OR RESID 301:301 ) )G301
12X-RAY DIFFRACTION8( CHAIN H AND RESID 10:133 )H10 - 133

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