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- PDB-2qd0: Crystal structure of mitoNEET -

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Basic information

Entry
Database: PDB / ID: 2qd0
TitleCrystal structure of mitoNEET
ComponentsZinc finger CDGSH domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / iron-sulfur cluster / [2FE-2S] / HISTIDINE LIGATION
Function / homology
Function and homology information


protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion ...protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion / identical protein binding / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsLin, J. / Zhou, T. / Ye, K. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of human mitoNEET reveals distinct groups of iron sulfur proteins.
Authors: Lin, J. / Zhou, T. / Ye, K. / Wang, J.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger CDGSH domain-containing protein 1
B: Zinc finger CDGSH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1114
Polymers18,7602
Non-polymers3522
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-52 kcal/mol
Surface area7610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.838, 59.139, 65.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains an intertwined homodimer which represents the biological assembly.

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Components

#1: Protein Zinc finger CDGSH domain-containing protein 1


Mass: 9379.791 Da / Num. of mol.: 2 / Fragment: residues 32-108, soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCD1, C10orf70 / Plasmid: PET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 95 / 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

Crystal
IDDensity Matthews3/Da)Density % sol (%)
12.2846.02
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8100 mM Tris-HCl, 18% PEG 3350 , 200 mM KI., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop7.4100 mM Tris-HCl, 30% PEG 2000 ,100 mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.5418
SYNCHROTRONSPring-8 BL41XU21
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEMay 19, 2006mirrors
ADSC QUANTUM 3152CCDJul 6, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionRedundancy: 9.6 % / Av σ(I) over netI: 17.3 / Number: 102047 / Rmerge(I) obs: 0.057 / Χ2: 1.3 / D res high: 2 Å / D res low: 20 Å / Num. obs: 10656 / % possible obs: 88.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.392010010.0431.82410.1
4.35.3910010.0391.58311.2
3.764.310010.0391.3711.5
3.423.7610010.0451.26411.4
3.173.4210010.0541.27211.4
2.993.1710010.0681.24411.5
2.842.9910010.0951.18611.4
2.712.8410010.1081.16311.2
2.612.7110010.1411.22810.9
2.522.6199.510.1551.22310.1
2.442.5299.510.1891.1449.8
2.372.4495.110.2411.1629.4
2.312.3791.610.2551.2278.8
2.252.3185.610.2711.328
2.22.2581.810.3061.1647.8
2.152.274.910.3041.1797.1
2.112.1569.710.3731.2926.4
2.072.1164.510.3121.4425.3
2.032.0754.810.3411.3084.5
22.0341.510.3541.1843.5
ReflectionResolution: 1.8→50 Å / Num. obs: 15523 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.045 / Χ2: 0.882 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.835.40.2166160.4841,276.8
1.83-1.8660.2056380.4881,281.7
1.86-1.95.80.1986910.5531,284.9
1.9-1.946.20.177180.6191,290.9
1.94-1.986.10.1367690.5691,294.1
1.98-2.036.30.1377740.6131,297.9
2.03-2.086.40.1237970.7741,299.6
2.08-2.136.70.1037960.6761,299.9
2.13-2.26.80.0878190.7391,2100
2.2-2.276.80.0867920.8591,2100
2.27-2.356.80.0718050.8691,2100
2.35-2.446.80.0718231.0011,2100
2.44-2.556.90.0677971.2231,2100
2.55-2.696.80.0697991.3141,2100
2.69-2.866.70.0668181.1061,2100
2.86-3.086.70.0598300.9991,2100
3.08-3.396.50.0488251.0041,2100
3.39-3.886.10.0358311.2281,299.8
3.88-4.886.30.0318391.0051,298
4.88-505.40.0367461.0751,282

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.29 Å / D res low: 19.65 Å / FOM : 0.311 / FOM acentric: 0.341 / FOM centric: 0 / Reflection: 13978
Phasing MAD setR cullis: 0.628 / R cullis acentric: 0.599 / R cullis centric: 10 / R kraut: 0.033 / R kraut acentric: 0.033 / R kraut centric: 0.03 / Highest resolution: 2.29 Å / Lowest resolution: 19.65 Å / FOM : 0.318 / FOM acentric: 0.351 / FOM centric: 0 / Loc: 6.118 / Loc acentric: 6.131 / Loc centric: 6.071 / Power: 1.763 kW / Power acentric: 1.711 / Power centric: 2.222
Phasing MAD setWavelength: 1.5418 Å / Atom type: FE / F double prime refined: 3.44 / F prime refined: -1.18
Phasing MAD set shell

R cullis centric: 10 / FOM centric: 0

IDResolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
14.56-19.650.3870.350.0290.0270.0380.4660.576.1576.1726.2293.4353.373.712
23.63-4.560.5230.4940.020.020.0180.4310.4835.6415.6465.6822.2552.2772.054
33.17-3.630.5780.5520.0230.0230.0260.4170.4584.9394.9414.9532.0242.0431.814
42.88-3.170.6760.6480.0320.0320.0290.3570.3895.2285.235.2531.5971.6071.478
52.68-2.880.7940.7650.0430.0440.0270.2810.3036.0246.0276.0571.1671.1771.029
62.52-2.680.8440.8130.0560.0570.0350.2140.2316.8586.8596.870.8680.8680.871
72.39-2.520.8680.8410.0720.0750.0290.1620.1727.1987.1997.2150.7070.7070.7
82.29-2.390.9090.8790.0830.0870.0310.130.1397.6137.6157.6350.5650.5670.525
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
4.56-19.650.45690.555901808
3.63-4.560.43050.482201846
3.17-3.630.41650.456901846
2.88-3.170.35530.385901827
2.68-2.880.27790.299201809
2.52-2.680.2090.224401794
2.39-2.520.1540.163101671
2.29-2.390.1240.131501377
Phasing dmDelta phi final: 9.34 / Delta phi initial: 64.82 / FOM : 0.919 / Mask type: RMS / Method: FLIP / Reflection: 14612
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.39-205.9310.9562093
3.49-4.397.0750.9512090
3.05-3.4910.7730.9042093
2.77-3.0510.8910.8582085
2.57-2.7710.2270.8592090
2.42-2.5710.1640.9142098
2.3-2.4210.3410.9952063

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.81→21.92 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.695 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 739 5 %RANDOM
Rwork0.164 ---
obs0.166 14902 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.944 Å2
Baniso -1Baniso -2Baniso -3
1-5.12 Å20 Å20 Å2
2---3.93 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.81→21.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 8 95 1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221160
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.941561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.06525.08559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19215226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.664155
X-RAY DIFFRACTIONr_chiral_restr0.1060.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02881
X-RAY DIFFRACTIONr_nbd_refined0.1920.2480
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.27
X-RAY DIFFRACTIONr_mcbond_it0.8031.5715
X-RAY DIFFRACTIONr_mcangle_it1.21421116
X-RAY DIFFRACTIONr_scbond_it1.9393504
X-RAY DIFFRACTIONr_scangle_it2.8774.5436
LS refinement shellResolution: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 22 -
Rwork0.209 787 -
obs-809 68.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.64966.8165-0.506922.2677-1.24597.38820.1119-0.499-0.25992.6620.1769-1.223-0.27240.3649-0.28870.05120.0608-0.1909-0.0411-0.0226-0.12929.064-5.917-7.689
21.7144.94141.961516.45362.78495.97560.1558-0.1479-0.39141.4182-0.11770.04510.2221-0.3308-0.0381-0.0720.0167-0.0187-0.0750.0277-0.10793.971-14.128-10.759
321.427-5.21326.74913.8053-1.43175.32210.00580.39960.0242-0.47440.07321.25330.1643-0.1322-0.079-0.2027-0.0368-0.0505-0.14430.0315-0.0585-4.984-8.613-19.727
422.65195.272713.527458.780833.919337.1218-0.2997-0.9151-0.641-3.5886-1.01023.6896-3.4214-1.78711.30990.27610.15480.06770.16290.17810.6959-16.587-1.502-19.112
50.2726-0.9212-1.258310.3212.0656.47170.17110.26320.04170.889-0.13781.22680.1454-0.0492-0.0333-0.18870.00030.1023-0.15430.0191-0.0561-4.1450.827-13.824
610.45943.41270.687715.3491.10137.0890.2693-0.63470.13142.02930.02140.28360.32680.0618-0.29080.13630.04640.0762-0.13460.0018-0.25230.883-3.371-6.674
74.10962.15824.550717.2059-5.236111.7753-0.0547-0.4401-0.20691.8360.08141.72690.2588-0.7258-0.0267-0.0812-0.03510.245-0.08710.0285-0.0307-5.929-3.361-8.843
825.897113.5006-0.63867.63512.499913.4575-0.0695-0.6544-0.06922.398-0.13130.33970.5258-0.23240.20070.34870.04340.0863-0.0453-0.0247-0.13981.2515.107-4.015
917.3152-1.29428.885731.5759-10.012323.3769-0.0316-0.99910.30233.35810.0304-0.9219-0.9736-0.26660.00120.26580.0353-0.1601-0.1172-0.0823-0.14377.0298.372-5.111
1030.86064.321616.46739.7143.42513.2975-0.35580.00850.8519-0.28030.00081.8048-0.3995-0.51230.355-0.18370.03640.0103-0.11080.03520.1444-8.9735.556-18.327
1115.8525-7.289425.23213.3518-11.602440.1615-0.25020.43160.5502-1.1134-0.59960.1426-0.79391.03230.84980.50810.0028-0.10240.43840.05210.154916.6493.885-0.666
125.1418-3.50790.676620.03724.58453.3453-0.06070.17940.41130.4010.1654-1.3415-0.06060.2453-0.1047-0.2196-0.004-0.0157-0.102-0.0172-0.04658.85910.295-15.258
1312.48424.18518.677611.83415.80998.7794-0.1468-0.06490.2034-0.2435-0.03641.1626-0.1268-0.19740.1832-0.2584-0.0181-0.0131-0.1527-0.0063-0.0313-4.1228.746-18.62
141.8132-0.74185.905942.672722.497933.88740.25880.4848-0.9345-2.502-0.88451.8644-1.09430.04170.62570.15020.0389-0.45630.0883-0.02560.2921-11.7812.128-28.899
156.413-1.38584.879712.0354-1.324910.2651-0.10480.271-0.0906-0.79760.19540.6807-0.1227-0.2492-0.0906-0.23770.0118-0.0292-0.12070.01-0.203-1.539-2.112-23.321
167.8193-2.14714.3418.63931.37337.76020.01980.21860.2097-0.43890.0787-0.7951-0.3650.6412-0.0984-0.1975-0.03410.0628-0.118-0.0152-0.13977.6873.028-21.308
177.9691-4.7653.512812.0682-3.28593.64850.14240.3046-0.0623-1.1281-0.0104-0.84630.09020.3792-0.132-0.1897-0.01060.0935-0.0887-0.0188-0.15958.142-2.743-23.017
1828.28443.7481-2.404824.06999.260928.23590.56070.7206-0.379-0.0939-0.0078-2.31890.29991.9752-0.5529-0.25840.0847-0.0461-0.0188-0.00670.127815.459-8.682-16.504
1914.1589-3.603311.99911.512-5.539110.75160.24290.2026-0.4410.05840.153-0.10140.2414-0.0366-0.3958-0.21080.05010.0164-0.1372-0.0373-0.19344.395-7.251-16.688
2034.7679-1.299511.018117.1731.987328.9208-0.17420.3921-1.3298-1.24090.00672.40450.39-1.61880.1676-0.0618-0.0375-0.298-0.0539-0.00050.2534-10.456-6.586-26.233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA43 - 4814 - 19
2X-RAY DIFFRACTION2AA49 - 5420 - 25
3X-RAY DIFFRACTION3AA55 - 6226 - 33
4X-RAY DIFFRACTION4AA63 - 6834 - 39
5X-RAY DIFFRACTION5AA69 - 7440 - 45
6X-RAY DIFFRACTION6AA75 - 7846 - 49
7X-RAY DIFFRACTION7AA79 - 8450 - 55
8X-RAY DIFFRACTION8AA85 - 9056 - 61
9X-RAY DIFFRACTION9AA91 - 9762 - 68
10X-RAY DIFFRACTION10AA98 - 10669 - 77
11X-RAY DIFFRACTION11BB38 - 449 - 15
12X-RAY DIFFRACTION12BB45 - 5416 - 25
13X-RAY DIFFRACTION13BB55 - 6126 - 32
14X-RAY DIFFRACTION14BB62 - 6733 - 38
15X-RAY DIFFRACTION15BB68 - 7339 - 44
16X-RAY DIFFRACTION16BB74 - 8045 - 51
17X-RAY DIFFRACTION17BB81 - 9052 - 61
18X-RAY DIFFRACTION18BB91 - 9562 - 66
19X-RAY DIFFRACTION19BB96 - 10167 - 72
20X-RAY DIFFRACTION20BB102 - 10673 - 77

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