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- PDB-3fnv: Crystal Structure of Miner1: The Redox-active 2Fe-2S Protein Caus... -

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Basic information

Entry
Database: PDB / ID: 3fnv
TitleCrystal Structure of Miner1: The Redox-active 2Fe-2S Protein Causative in Wolfram Syndrome 2
ComponentsCDGSH iron sulfur domain-containing protein 2
KeywordsMETAL BINDING PROTEIN / diabetes / membrane bound / thiazolidinedione / oxidative stress / CDGSH / Endoplasmic reticulum / Iron / Iron-sulfur / Membrane / Metal-binding / Transmembrane / Zinc-finger
Function / homology
Function and homology information


perinuclear endoplasmic reticulum / autophagy of mitochondrion / regulation of autophagy / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / RNA binding ...perinuclear endoplasmic reticulum / autophagy of mitochondrion / regulation of autophagy / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / RNA binding / membrane / metal ion binding
Similarity search - Function
CDGSH iron-sulfur domain, mitoNEET-type / Iron sulphur domain-containing, mitoNEET, N-terminal / Iron-containing outer mitochondrial membrane protein N-terminus / CDGSH iron-sulfur domain-containing protein 1/2 / Iron-binding zinc finger CDGSH type / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain / CDGSH-type zinc finger. Function unknown. / Ribosomal Protein L9; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / CDGSH iron-sulfur domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsConlan, A.R. / Axelrod, H.L. / Cohen, A.E. / Abresch, E.C. / Yee, D. / Zuris, J. / Nechushtai, R. / Jennings, P.A. / Paddock, M.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of Miner1: The redox-active 2Fe-2S protein causative in Wolfram Syndrome 2.
Authors: Conlan, A.R. / Axelrod, H.L. / Cohen, A.E. / Abresch, E.C. / Zuris, J. / Yee, D. / Nechushtai, R. / Jennings, P.A. / Paddock, M.L.
History
DepositionDec 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDGSH iron sulfur domain-containing protein 2
B: CDGSH iron sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3324
Polymers18,9802
Non-polymers3522
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-18 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.904, 48.579, 74.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Auth seq-ID: 68 - 500 / Label seq-ID: 68 - 500

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a dimer formed from the two chains (A and B) in the crystallographic asymmetric unit.

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Components

#1: Protein CDGSH iron sulfur domain-containing protein 2 / Endoplasmic reticulum intermembrane small protein / MitoNEET-related 1 protein / Miner1


Mass: 9490.047 Da / Num. of mol.: 2
Fragment: C-terminal water-soluble domain: UNP residues 57-135
Mutation: C92S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDGSH2, CISD2, ERIS, ZCD2 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5K1
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. IN THE TARGET SEQUENCE, CYS 92 IS REPLACED BY AN SER RESIDUE BY SITE-DIRECTED MUTAGENESIS. 2. ...1. IN THE TARGET SEQUENCE, CYS 92 IS REPLACED BY AN SER RESIDUE BY SITE-DIRECTED MUTAGENESIS. 2. THE SOLUBLE DOMAIN OF MINER1 (RESIDUES 57-135) WAS EXPRESSED WITH A PURIFICATION TAG IN A PET28A(+) (NOVAGEN) BACTERIAL EXPRESSION VECTOR CONTAINING AN N-TERMINAL HIS-TAG. THE TAG WAS REMOVED WITH THROMBIN LEAVING ONLY GSHM FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.94 Å3/Da / Density % sol: 36.58 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8
Details: 100 mM Tris-HCl pH 8.0, 100 mM NaCl, 15% PEG 3000, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.7418, 1.3624, 1.7372
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.74181
21.36241
31.73721
ReflectionNumber: 217494 / Rmerge(I) obs: 0.139 / D res high: 2.16 Å / Num. obs: 8210 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.162.2476592.511.244
2.242.3379696.510.957
2.332.437519710.682
2.432.568369810.523
2.562.7279898.310.335
2.722.9381698.910.23
2.933.2282099.310.146
3.223.6984598.910.104
3.694.6485499.410.081
4.6448.5692999.510.075
ReflectionResolution: 1.8→48.56 Å / Num. obs: 14086 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 25.9 % / Biso Wilson estimate: 34.594 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 16.17
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 17.9 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 18126 / Num. unique obs: 1285 / % possible all: 97.9

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
119.71311.80813.092FE28.881.39
28.48532.0115.36FE36.041.61
322.17312.90113.254FE33.731.57
47.94832.99812.912FE36.431.54
510.07930.35716.688FE34.060.14
Phasing dmFOM : 0.8 / FOM acentric: 0.81 / FOM centric: 0.74 / Reflection: 9018 / Reflection acentric: 7562 / Reflection centric: 1456
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-29.4610.980.990.95439270169
3.8-60.960.980.911242962280
3-3.80.930.950.8615261259267
2.6-30.870.880.7615191295224
2.3-2.60.730.750.5926582325333
2.1-2.30.560.580.416341451183

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→37.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.928 / SU B: 7.676 / SU ML: 0.101 / SU R Cruickshank DPI: 0.208 / SU Rfree: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.164
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. AN 2FE-2S CLUSTER (FES) WAS MODELED INTO EACH SUBUNIT IN THE ASYMMETRIC UNIT. THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. AN 2FE-2S CLUSTER (FES) WAS MODELED INTO EACH SUBUNIT IN THE ASYMMETRIC UNIT. THE PRESENCE OF THE 2FE-2S CLUSTER WAS CORROBORATED BY ANOMALOUS DIFFERENCE MAPS. THE PROTEIN LIGANDS TO THE FE ATOMS IN THE 2FE-2S CLUSTERS ARE CYS 99, CYS 101, CYS 110, AND HIS 114.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 450 5 %RANDOM
Rwork0.17 ---
obs0.172 9013 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.35 Å2 / Biso mean: 35.795 Å2 / Biso min: 16.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---1.52 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 8 40 1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221056
X-RAY DIFFRACTIONr_bond_other_d0.0010.02683
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9631440
X-RAY DIFFRACTIONr_angle_other_deg0.90431695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1445141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46225.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83515176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.142154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_nbd_refined0.2080.3181
X-RAY DIFFRACTIONr_nbd_other0.20.3726
X-RAY DIFFRACTIONr_nbtor_refined0.1760.5510
X-RAY DIFFRACTIONr_nbtor_other0.0890.5541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.598
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1430.36
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.58
X-RAY DIFFRACTIONr_mcbond_it1.8033731
X-RAY DIFFRACTIONr_mcbond_other0.53272
X-RAY DIFFRACTIONr_mcangle_it2.53651106
X-RAY DIFFRACTIONr_scbond_it4.0888400
X-RAY DIFFRACTIONr_scangle_it5.41911326
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 775 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.350.5
MEDIUM THERMAL0.752
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 46 -
Rwork0.158 611 -
all-657 -
obs--98.65 %
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)
13.9833-0.79861.14976.6573-0.5854.60430.03620.01630.26160.061-0.044-0.1399-0.19580.04590.0078-0.1805-0.02-0.0262-0.2193-0.0182-0.151917.758638.141919.8189
24.2904-0.59091.48345.9646-1.6283.0652-0.01410.2092-0.1759-0.3546-0.02760.05540.3446-0.01960.0417-0.1464-0.0213-0.0193-0.1892-0.0293-0.155813.063730.890815.2213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 134
2X-RAY DIFFRACTION2B68 - 135

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