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- PDB-5vxa: Structure of the human Mesh1-NADPH complex -

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Basic information

Entry
Database: PDB / ID: 5vxa
TitleStructure of the human Mesh1-NADPH complex
ComponentsGuanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
KeywordsHYDROLASE / Mesh1 NADPH
Function / homology
Function and homology information


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / metal ion binding
Similarity search - Function
HD domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-NDP / Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsRose, J. / Zhou, P.
Citation
Journal: Nat Metab / Year: 2020
Title: MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis.
Authors: Ding, C.C. / Rose, J. / Sun, T. / Wu, J. / Chen, P.H. / Lin, C.C. / Yang, W.H. / Chen, K.Y. / Lee, H. / Xu, E. / Tian, S. / Akinwuntan, J. / Zhao, J. / Guan, Z. / Zhou, P. / Chi, J.T.
#1: Journal: Biorxiv / Year: 2018
Title: Mammalian stringent-like response mediated by the cytosolic NADPH phosphatase MESH1
Authors: Ding, C.-K.C. / Rose, J. / Zhou, P. / Chi, J.-T.A.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.3Mar 30, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_comp_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.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
B: Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,13813
Polymers41,0292
Non-polymers2,10911
Water4,612256
1
A: Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5507
Polymers20,5141
Non-polymers1,0366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5876
Polymers20,5141
Non-polymers1,0735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-93 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.780, 80.370, 114.460
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 , 1 types, 2 molecules AB

#1: Protein Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 / HD domain-containing protein 3 / Metazoan SpoT homolog 1 / MESH1 / Penta-phosphate guanosine-3'- ...HD domain-containing protein 3 / Metazoan SpoT homolog 1 / MESH1 / Penta-phosphate guanosine-3'-pyrophosphohydrolase / (ppGpp)ase


Mass: 20514.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDDC3, MESH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N4P3, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase

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Non-polymers , 7 types, 267 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4.5 mg/mL hMesh1 D66K, 50 mM NADPH, 25 mM Tris (pH 8.0), 100 mM NaCl, 0.05% 2-mercaptoethanol, 0.5 mM ZnCl2, 100 mM ammonium acetate, 50 mM sodium citrate, 12.5% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.07 Å / Num. obs: 26452 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 17.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.1→41.07 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.2055 1342 5.07 %
Rwork0.1654 --
obs0.1675 26449 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 110 256 3175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083082
X-RAY DIFFRACTIONf_angle_d0.9724185
X-RAY DIFFRACTIONf_dihedral_angle_d13.6411859
X-RAY DIFFRACTIONf_chiral_restr0.051467
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.23931340.19652491X-RAY DIFFRACTION100
2.1751-2.26210.24641270.19392430X-RAY DIFFRACTION100
2.2621-2.36510.22311170.18252492X-RAY DIFFRACTION100
2.3651-2.48980.20371150.1732501X-RAY DIFFRACTION100
2.4898-2.64570.22931460.17072475X-RAY DIFFRACTION100
2.6457-2.850.2271360.17142486X-RAY DIFFRACTION100
2.85-3.13670.19951370.17222494X-RAY DIFFRACTION100
3.1367-3.59030.18381400.152528X-RAY DIFFRACTION100
3.5903-4.52250.19981480.13142529X-RAY DIFFRACTION100
4.5225-41.07820.17831420.17312681X-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)
13.03981.61580.07863.7780.03151.89570.00440.0199-0.0770.16050.035-0.2276-0.10050.1768-0.05210.0895-0.0176-0.01690.12310.0020.073911.5487-17.2402-36.5393
21.20990.02370.17651.99640.91031.59480.1655-0.07280.15060.5111-0.1454-0.1105-0.31030.1182-0.00340.2277-0.0898-0.01610.1084-0.00450.099610.5556-9.1012-28.166
32.69050.3937-0.45991.8542-0.49041.19490.1542-0.2963-0.41980.5995-0.093-0.7962-0.12930.5232-0.0970.2267-0.0783-0.20040.34740.0450.306622.138-18.1818-27.288
43.34821.2806-1.26942.3773-0.96390.5944-0.4502-0.1915-0.61090.349-0.2046-0.4136-0.34090.5140.3090.4268-0.1049-0.12530.32830.1040.245214.1163-25.9682-15.0607
51.46990.3684-0.13241.4776-0.49641.28540.1295-0.01040.07350.7398-0.06170.29250.0069-0.0109-0.07280.3482-0.02850.04850.11630.00640.10041.423-20.6966-19.8615
63.23882.3593-0.32972.79320.58130.6714-0.0955-0.6178-0.14870.7427-0.12260.5586-0.6023-0.07190.00490.49880.10720.46580.0438-0.379-0.6019-1.1287-12.0896-13.9685
71.19240.1041-0.00691.82950.13151.17730.07440.0330.1490.0291-0.01850.0094-0.1792-0.0339-0.0450.0831-0.0050.04090.08570.00080.10216.4394-6.6773-44.2963
82.94720.41540.80340.81091.54343.29990.3610.54850.1956-0.2545-0.27570.4864-0.3547-0.5504-0.07610.28350.12980.06230.28310.11870.30363.5074-4.5255-63.3397
91.2209-0.0290.17961.62020.37240.91640.21710.1699-0.0728-0.077-0.0849-0.0889-0.0813-0.0634-0.03260.07730.01610.0660.17910.00940.145614.429-13.7202-59.4831
100.6943-0.6874-0.85093.31661.91641.50260.10710.08340.2465-0.11020.0796-0.305-0.22750.3143-0.13160.1163-0.01490.09080.2198-0.01330.199523.914-7.2573-60.3701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 89 )
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 179 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 112 )
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 157 )
10X-RAY DIFFRACTION10chain 'B' and (resid 158 through 179 )

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