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- PDB-4f1e: The Crystal Structure of a Human MitoNEET mutant with Asp 67 repl... -

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Basic information

Entry
Database: PDB / ID: 4f1e
TitleThe Crystal Structure of a Human MitoNEET mutant with Asp 67 replaced by a Gly
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / ZINC Finger CDGSH-Type domain 1 / mitochondrial outer membrane
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBaxter, E.I. / Zuris, J.A. / Wang, C. / Axelrod, H.L. / Cohen, A.E. / Paddock, M.L. / Nechushtai, R. / Onuchic, J.N. / Jennings, P.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Allosteric control in a metalloprotein dramatically alters function.
Authors: Baxter, E.L. / Zuris, J.A. / Wang, C. / Vo, P.L. / Axelrod, H.L. / Cohen, A.E. / Paddock, M.L. / Nechushtai, R. / Onuchic, J.N. / Jennings, P.A.
History
DepositionMay 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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

Downloads & links

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Assembly

Deposited unit
A: CDGSH iron-sulfur domain-containing protein 1
B: CDGSH iron-sulfur domain-containing protein 1
C: CDGSH iron-sulfur domain-containing protein 1
D: CDGSH iron-sulfur domain-containing protein 1
E: CDGSH iron-sulfur domain-containing protein 1
F: CDGSH iron-sulfur domain-containing protein 1
G: CDGSH iron-sulfur domain-containing protein 1
H: CDGSH iron-sulfur domain-containing protein 1
I: CDGSH iron-sulfur domain-containing protein 1
J: CDGSH iron-sulfur domain-containing protein 1
K: CDGSH iron-sulfur domain-containing protein 1
L: CDGSH iron-sulfur domain-containing protein 1
M: CDGSH iron-sulfur domain-containing protein 1
N: CDGSH iron-sulfur domain-containing protein 1
O: CDGSH iron-sulfur domain-containing protein 1
P: CDGSH iron-sulfur domain-containing protein 1
Q: CDGSH iron-sulfur domain-containing protein 1
R: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,19036
Polymers160,02518
Non-polymers3,16518
Water1,60389
1
A: CDGSH iron-sulfur domain-containing protein 1
B: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-17 kcal/mol
Surface area6750 Å2
MethodPISA
2
C: CDGSH iron-sulfur domain-containing protein 1
D: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-19 kcal/mol
Surface area6890 Å2
MethodPISA
3
E: CDGSH iron-sulfur domain-containing protein 1
F: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-17 kcal/mol
Surface area6800 Å2
MethodPISA
4
G: CDGSH iron-sulfur domain-containing protein 1
H: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-16 kcal/mol
Surface area6900 Å2
MethodPISA
5
I: CDGSH iron-sulfur domain-containing protein 1
J: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-21 kcal/mol
Surface area6770 Å2
MethodPISA
6
K: CDGSH iron-sulfur domain-containing protein 1
L: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-19 kcal/mol
Surface area6750 Å2
MethodPISA
7
M: CDGSH iron-sulfur domain-containing protein 1
N: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-19 kcal/mol
Surface area6780 Å2
MethodPISA
8
O: CDGSH iron-sulfur domain-containing protein 1
P: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-14 kcal/mol
Surface area6700 Å2
MethodPISA
9
Q: CDGSH iron-sulfur domain-containing protein 1
R: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1324
Polymers17,7812
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-16 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.396, 110.855, 207.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CDGSH iron-sulfur domain-containing protein 1 / MitoNEET


Mass: 8890.291 Da / Num. of mol.: 18 / Fragment: Water-soluble domain, UNP residues 33-108 / Mutation: D67G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf70, CISD1, MDS029, ZCD1 / Plasmid: pET28-a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q9NZ45
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.02 Å3/Da / Density % sol: 39.25 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2009
Details: Double crystal monochromator Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→49.54 Å / Num. obs: 51597 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 62.343 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.490.7541.8719676507094.8
2.49-2.580.6153.0525180461199.7
2.58-2.70.4664.57344145260100
2.7-2.840.3286.26332505058100
2.84-3.020.2089.0834252519999.9
3.02-3.250.12213.53335365102100
3.25-3.580.0719.99345105269100
3.58-4.090.0526.57336375154100
4.09-5.140.04431.4834129529099.9
5.140.04933.5134113558499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.28 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.54 Å
Translation3 Å49.54 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2QH7

2qh7


Resolution: 2.4→49.54 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9293 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). .
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2624 5.09 %RANDOM
Rwork0.1933 ---
obs0.195 51524 --
Displacement parametersBiso max: 177.23 Å2 / Biso mean: 74.0283 Å2 / Biso min: 30.13 Å2
Baniso -1Baniso -2Baniso -3
1-6.748 Å20 Å20 Å2
2--7.8559 Å20 Å2
3----14.6039 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9078 0 72 89 9239
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4387SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes233HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1346HARMONIC5
X-RAY DIFFRACTIONt_it9369HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1197SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10380SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9369HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12574HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion1.82
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2434 177 4.99 %
Rwork0.2419 3370 -
all0.2419 3547 -
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)
17.0839-0.911-0.10234.45580.05361.44490.03720.02040.5535-0.3295-0.0513-0.1214-0.14930.33160.0141-0.06990.05960.001-0.112-0.00040.07530.48187.945212.0562
26.4318-1.9368-0.05043.2086-0.60451.6296-0.0605-0.47030.2810.26970.1357-0.1207-0.30420.2589-0.0752-0.07370.07940.0006-0.0572-0.07510.03910.31255.260621.5835
31.89011.0553-0.78295.29550.09873.14580.1476-0.3372-0.04580.5858-0.2883-0.3128-0.01010.17620.14070.1132-0.2864-0.1499-0.16570.0293-0.0082-17.1261-19.805-6.0871
43.10951.8251-1.61375.4929-1.41883.11670.01990.04210.56540.3496-0.16250.66030.0615-0.10730.1427-0.032-0.19880.0297-0.2277-0.04160.1869-25.4591-17.6267-10.6694
58.2751-1.65991.2562.5588-0.29731.71220.0274-0.2404-0.1948-0.1662-0.01440.07230.02010.2011-0.013-0.2223-0.04150.09810.18250.0064-0.1189-37.0995-0.448943.4797
65.814-1.34471.31011.06590.25062.7821-0.0430.05750.3779-0.30370.0798-0.105-0.04520.3141-0.0368-0.205-0.12330.0610.175-0.0051-0.0668-31.32796.912340.1488
73.5316-0.1559-1.59133.2112-0.75334.2612-0.0464-0.33090.09590.37430.1482-0.234-0.0944-0.1236-0.10190.16390.29490.1258-0.25010.043-0.0013-27.513740.267826.9543
83.41-0.0451-0.7434.1522-1.41764.504-0.0305-0.1795-0.28750.0480.01610.44070.0277-0.19130.01440.08780.29640.2874-0.24860.14820.0652-33.495935.065321.0585
94.17350.39110.18744.9842-0.60891.4570.0009-0.092-0.2224-0.0142-0.2157-0.4071-0.07640.26160.2148-0.0699-0.1759-0.094-0.18660.08470.1711-1.072-11.225-14.9288
102.94630.1059-0.22754.4329-0.14952.0789-0.0771-0.0148-0.1038-0.26-0.08-0.4988-0.13180.18210.1571-0.0803-0.2353-0.0519-0.14510.09970.15663.1563-3.6708-19.7035
113.63560.1559-1.76537.7393-0.86951.851-0.0822-0.0535-0.33740.58850.11480.64550.04890.0213-0.0327-0.020.19310.1121-0.22610.07260.0914-3.55-23.004922.499
121.0383-0.0056-1.12725.29620.11233.2426-0.1069-0.0872-0.03650.79390.19890.38380.01360.0867-0.0920.07860.26230.1205-0.15660.08070.0104-3.81-13.408725.6066
132.3995-0.86651.2555.0653-1.41713.23190.14930.3166-0.0131-0.4024-0.1312-0.0255-0.1139-0.0463-0.01810.0270.27740.0926-0.2053-0.00060.1155-16.189616.93166.3506
142.3735-1.6476-0.3935.0108-0.70871.39740.12170.2112-0.084-0.2988-0.15710.403-0.2345-0.13060.0355-0.02330.22920.0281-0.2143-0.02020.1561-24.182622.70298.1726
154.6262-3.9732-2.24491.4439-0.13882.2626-0.1346-0.2440.50750.0027-0.0377-0.1049-0.1777-0.0260.1723-0.3258-0.0338-0.16790.1327-0.22850.2267-18.428713.414952.5095
165.17031.105-1.93661.73051.07041.0357-0.1058-0.34690.31240.1223-0.0423-0.2326-0.1549-0.04190.1481-0.44780.0447-0.1710.4609-0.28530.0748-12.527913.251960.943
173.84293.0594-1.57791.79791.38624.6584-0.1298-0.4871-0.2490.26090.08940.20360.17720.05670.0405-0.42840.1030.12870.47470.1362-0.21510.1709-0.754960.1689
182.69080.00152.22792.8777-0.31171.4722-0.0838-0.2565-0.30860.08790.01020.01260.17310.21760.0735-0.34620.10010.26510.24040.20630.14855.9814-7.579755.3607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|42-106 }0
2X-RAY DIFFRACTION2{ B|43-107 }0
3X-RAY DIFFRACTION3{ C|42-107 }0
4X-RAY DIFFRACTION4{ D|43-107 }0
5X-RAY DIFFRACTION5{ E|42-106 }0
6X-RAY DIFFRACTION6{ F|42-106 }0
7X-RAY DIFFRACTION7{ G|42-107 }0
8X-RAY DIFFRACTION8{ H|43-108 }0
9X-RAY DIFFRACTION9{ I|42-106 }0
10X-RAY DIFFRACTION10{ J|41-106 }0
11X-RAY DIFFRACTION11{ K|42-107 }0
12X-RAY DIFFRACTION12{ L|43-106 }0
13X-RAY DIFFRACTION13{ M|42-106 }0
14X-RAY DIFFRACTION14{ N|42-106 }0
15X-RAY DIFFRACTION15{ O|46-107 }0
16X-RAY DIFFRACTION16{ P|44-106 }0
17X-RAY DIFFRACTION17{ Q|44-107 }0
18X-RAY DIFFRACTION18{ R|44-107 }0

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