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- PDB-6tc0: Crystal structure of MMS19-CIAO1-CIAO2B CIA targeting complex -

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Basic information

Entry
Database: PDB / ID: 6tc0
TitleCrystal structure of MMS19-CIAO1-CIAO2B CIA targeting complex
Components
  • MIP18 family protein galla-2
  • MMS19 nucleotide excision repair protein homolog
  • Probable cytosolic iron-sulfur protein assembly protein Ciao1
KeywordsCYTOSOLIC PROTEIN / Fe-S cluster / Fe-S / CIA / CIA core complex
Function / homology
Function and homology information


cytosolic [4Fe-4S] assembly targeting complex / protein maturation by [4Fe-4S] cluster transfer / protein maturation by iron-sulfur cluster transfer / MMXD complex / iron-sulfur cluster assembly / DNA metabolic process / positive regulation of double-strand break repair via homologous recombination / chromosome segregation / nuclear estrogen receptor binding / spindle ...cytosolic [4Fe-4S] assembly targeting complex / protein maturation by [4Fe-4S] cluster transfer / protein maturation by iron-sulfur cluster transfer / MMXD complex / iron-sulfur cluster assembly / DNA metabolic process / positive regulation of double-strand break repair via homologous recombination / chromosome segregation / nuclear estrogen receptor binding / spindle / transcription coactivator activity / cell division / DNA repair / DNA damage response / positive regulation of DNA-templated transcription / enzyme binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Probable cytosolic iron-sulfur protein assembly protein, CIAO1/Cia1 / MMS19, C-terminal / MMS19, N-terminal / MIP18 family / DNA repair/transcription protein MET18/MMS19 / RNAPII transcription regulator C-terminal / Dos2-interacting transcription regulator of RNA-Pol-II / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily ...Probable cytosolic iron-sulfur protein assembly protein, CIAO1/Cia1 / MMS19, C-terminal / MMS19, N-terminal / MIP18 family / DNA repair/transcription protein MET18/MMS19 / RNAPII transcription regulator C-terminal / Dos2-interacting transcription regulator of RNA-Pol-II / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Probable cytosolic iron-sulfur protein assembly protein Ciao1 / MMS19 nucleotide excision repair protein homolog / MIP18 family protein galla-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsKassube, S.A. / Thoma, N.H.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 871-2014 Switzerland
Swiss National Science FoundationCRSII3_160734 Switzerland
European Research Council (ERC)666068 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural insights into Fe-S protein biogenesis by the CIA targeting complex.
Authors: Susanne A Kassube / Nicolas H Thomä /
Abstract: The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. ...The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. The molecular mechanisms of client protein recognition and Fe-S cluster transfer remain unknown. Here, we report crystal structures of the CIA targeting complex (CTC), revealing that its CIAO2B subunit is centrally located and bridges CIAO1 and the client adaptor protein MMS19. Cryo-EM reconstructions of human CTC bound either to the DNA replication factor primase or to the DNA helicase DNA2, combined with biochemical, biophysical and yeast complementation assays, reveal an evolutionarily conserved, bipartite client recognition mode facilitated by CIAO1 and the structural flexibility of the MMS19 subunit. Unexpectedly, the primase Fe-S cluster is located ~70 Å away from the CTC reactive cysteine, implicating conformational dynamics of the CTC or additional maturation factors in the mechanism of Fe-S cluster transfer.
History
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable cytosolic iron-sulfur protein assembly protein Ciao1
B: MIP18 family protein galla-2
C: MMS19 nucleotide excision repair protein homolog
D: Probable cytosolic iron-sulfur protein assembly protein Ciao1
E: MIP18 family protein galla-2
F: MMS19 nucleotide excision repair protein homolog


Theoretical massNumber of molelcules
Total (without water)337,2476
Polymers337,2476
Non-polymers00
Water00
1
A: Probable cytosolic iron-sulfur protein assembly protein Ciao1
B: MIP18 family protein galla-2
C: MMS19 nucleotide excision repair protein homolog


Theoretical massNumber of molelcules
Total (without water)168,6233
Polymers168,6233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Probable cytosolic iron-sulfur protein assembly protein Ciao1
E: MIP18 family protein galla-2
F: MMS19 nucleotide excision repair protein homolog


Theoretical massNumber of molelcules
Total (without water)168,6233
Polymers168,6233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16660 Å2
ΔGint-27 kcal/mol
Surface area126400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.400, 140.700, 327.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLUGLUchain 'A'AA0 - 3353 - 338
221GLYGLYGLUGLUchain 'D'DD0 - 3353 - 338
132PROPROLYSLYSchain 'B'BB2 - 1555 - 158
242PROPROLYSLYSchain 'E'EE2 - 1555 - 158
153GLYGLYSERSER(chain 'C' and (resid 15 through 695 or resid 702 through 1028))CC15 - 4219 - 46
163THRTHRSERSER(chain 'C' and (resid 15 through 695 or resid 702 through 1028))CC46 - 53950 - 543
173THRTHRPROPRO(chain 'C' and (resid 15 through 695 or resid 702 through 1028))CC548 - 638552 - 642
183LEULEUGLUGLU(chain 'C' and (resid 15 through 695 or resid 702 through 1028))CC649 - 695653 - 699
193PHEPHESERSER(chain 'C' and (resid 15 through 695 or resid 702 through 1028))CC702 - 1028706 - 1032
2103GLYGLYSERSER(chain 'F' and (resid 15 through 695 or resid 702 through 1028))FF15 - 4219 - 46
2113THRTHRSERSER(chain 'F' and (resid 15 through 695 or resid 702 through 1028))FF46 - 53950 - 543
2123THRTHRPROPRO(chain 'F' and (resid 15 through 695 or resid 702 through 1028))FF548 - 638552 - 642
2133LEULEUGLUGLU(chain 'F' and (resid 15 through 695 or resid 702 through 1028))FF649 - 695653 - 699
2143PHEPHESERSER(chain 'F' and (resid 15 through 695 or resid 702 through 1028))FF702 - 1028706 - 1032

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Probable cytosolic iron-sulfur protein assembly protein Ciao1


Mass: 37283.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ciao1, CG12797 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7K1Y4
#2: Protein MIP18 family protein galla-2


Mass: 17806.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: galla-2, CG7949 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VTC4
#3: Protein MMS19 nucleotide excision repair protein homolog / MET18 homolog / MMS19-like protein


Mass: 113534.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mms19, Mms19l / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9D071

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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: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. obs: 111722 / % possible obs: 98.4 % / Redundancy: 41.4 % / Biso Wilson estimate: 174.76 Å2 / CC1/2: 1 / Net I/σ(I): 12
Reflection shellResolution: 3.6→3.73 Å / Num. unique obs: 11172 / CC1/2: 0.124

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Processing

Software
NameVersionClassification
CNSrefinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.6→20 Å / SU ML: 0.6952 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.5082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2771 5535 5.02 %
Rwork0.2581 104820 -
obs0.2591 110355 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 211.22 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22972 0 0 0 22972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008823437
X-RAY DIFFRACTIONf_angle_d1.31231862
X-RAY DIFFRACTIONf_chiral_restr0.07773733
X-RAY DIFFRACTIONf_plane_restr0.00914097
X-RAY DIFFRACTIONf_dihedral_angle_d16.696214214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.640.4251850.38943473X-RAY DIFFRACTION99.95
3.64-3.680.3981870.3843550X-RAY DIFFRACTION99.97
3.68-3.730.42331850.38493449X-RAY DIFFRACTION100
3.73-3.770.41761820.37663462X-RAY DIFFRACTION99.97
3.77-3.820.36051830.37183547X-RAY DIFFRACTION100
3.82-3.880.39971830.3723478X-RAY DIFFRACTION100
3.88-3.930.35791820.35893507X-RAY DIFFRACTION99.97
3.93-3.990.35251840.35313489X-RAY DIFFRACTION99.97
3.99-4.050.34971710.34843483X-RAY DIFFRACTION100
4.05-4.120.35691820.34423567X-RAY DIFFRACTION99.97
4.12-4.190.38151990.34123422X-RAY DIFFRACTION100
4.19-4.260.39671740.31513514X-RAY DIFFRACTION100
4.26-4.340.32261860.30393500X-RAY DIFFRACTION100
4.34-4.430.29681930.30963502X-RAY DIFFRACTION99.97
4.43-4.530.31231910.29233468X-RAY DIFFRACTION100
4.53-4.630.28121830.28973492X-RAY DIFFRACTION100
4.63-4.750.26851810.29023488X-RAY DIFFRACTION100
4.75-4.870.33762010.28713497X-RAY DIFFRACTION100
4.87-5.010.32961770.28343502X-RAY DIFFRACTION100
5.01-5.170.32471950.29033474X-RAY DIFFRACTION100
5.17-5.350.30461800.30923519X-RAY DIFFRACTION100
5.35-5.560.36381850.30783482X-RAY DIFFRACTION100
5.56-5.810.36831770.31393500X-RAY DIFFRACTION100
5.81-6.110.32831840.30663517X-RAY DIFFRACTION100
6.11-6.480.32721870.30623451X-RAY DIFFRACTION100
6.48-6.960.34991800.2883499X-RAY DIFFRACTION100
6.96-7.620.2541820.25423521X-RAY DIFFRACTION100
7.62-8.650.19811830.20693479X-RAY DIFFRACTION100
8.65-10.620.1821870.14793511X-RAY DIFFRACTION100
10.62-200.19751860.1893477X-RAY DIFFRACTION99.51
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)
13.135409141561.191780182-1.023257161346.72082150708-1.584204869014.967470626020.06562895422470.446227337069-0.65433835760.00332974835845-0.1213404057050.08836493972410.976248922287-1.19672172401-2.36508325236E-101.818674364430.0577333837994-0.2255327983292.53629969061-0.0718691242371.543731991121.80094512443-53.56742618293.80433198099
23.574970037160.214581636631.137501151075.923240122660.6857444446324.035662511760.1464685252690.3521237068640.569743881998-0.404867313246-0.0508523187223-0.189080112313-0.7584713886270.0710880991333-0.0284705966522.157480532260.0765403728374-0.2930735288792.610392096580.365892602821.6458753202816.7434065486-29.3313441714-17.1456600659
31.01101098393-1.540601080790.143268934622.6043500205-0.1157352986671.12960585683-0.223865433314-0.3996887061120.4467485513820.2228324336740.44885942574-0.4904587265020.1513294990770.242129582487-0.1649818303210.922109087343-0.112390200983-0.06439611944940.9137632626610.03490177653240.9374388598316.2610859427-24.7118937406-61.8241905111
41.15619323130.184618341612.170230406211.114998152471.250313918610.556234971862-1.56225043418-1.120418861262.152681444861.279391188010.620574217134-2.41823262269-0.592858773573-0.419725921078-2.49133203075E-95.088795693420.551918180217-1.268507113484.07986517878-0.5553824120574.8247841106328.510234150521.81544193750.172568775514
50.862077039277-1.74366781579-3.214291811014.89469078248-2.246947438333.46346874713-0.9070141788380.1283757543890.1938639378991.26896777581.2469619784-0.120706802593-0.419962013412-0.448638494804-0.1059049044463.379394636150.186577740279-0.2071616538183.05419743114-0.04775100381541.957609678055.95655846515-1.81074386392-14.7897119202
60.521614858829-0.6187582063290.03552901014581.435326785510.4319348437851.17342262213-0.207455032829-0.3859264671660.01485871662960.3767466663650.295163183772-0.0177158064135-0.0944089686095-0.127731685341-0.0244731654030.712604905046-0.0734485123776-0.1946326605220.855641289858-0.0489808584490.721962439027-8.41133077395-6.39252766063-57.170891017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 335)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 155)
3X-RAY DIFFRACTION3(chain 'C' and resid 18 through 1028)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 335)
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 155)
6X-RAY DIFFRACTION6(chain 'F' and resid 18 through 1028)

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