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- PDB-9chy: Crystal structure of the human MESH1 (D66K)-PAPS complex -

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Basic information

Entry
Database: PDB / ID: 9chy
TitleCrystal structure of the human MESH1 (D66K)-PAPS complex
ComponentsGuanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
KeywordsHYDROLASE / phosphatase / PAPS
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 / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
ACETIC ACID / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRose, J. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: MESH1 Functions as a Metazoan PAPS Phosphatase to Regulate Sulfation.
Authors: Lin, C.-C. / Rose, J. / Zhang, A. / Mirando, A.J. / Mestre, A.A. / Ding, C.C. / Liao, Y. / Chen, S.-Y. / Setayeshpour, Y. / Wu, J. / Li, Z. / Yan, D. / Hilton, M.J. / Zhou, P. / Chi, J.-T.
History
DepositionJul 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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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)42,2968
Polymers41,0292
Non-polymers1,2676
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.950, 71.700, 75.920
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

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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 / Mutation: D66K
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 , 5 types, 315 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4.5 mg/ml protein, 12.5 mM pAps, 25 mM Tris, pH 8.0, 100 mM NaCl, 0.05% 2-mercaptoethanol, 75 mM ammonium acetate, 50 mM sodium citrate, and 12.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→39.89 Å / Num. obs: 27172 / % possible obs: 99.44 % / Redundancy: 7.1 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.98
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 2655 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.89 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 1360 5.01 %
Rwork0.172 25800 -
obs0.1743 27160 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 72 309 3205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282966
X-RAY DIFFRACTIONf_angle_d0.64984033
X-RAY DIFFRACTIONf_chiral_restr0.0401455
X-RAY DIFFRACTIONf_plane_restr0.0048522
X-RAY DIFFRACTIONf_dihedral_angle_d8.2004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.29241320.26142521X-RAY DIFFRACTION98.96
1.97-2.050.25151340.19352531X-RAY DIFFRACTION98.74
2.05-2.140.21321330.17622526X-RAY DIFFRACTION99.33
2.14-2.250.21381330.17462537X-RAY DIFFRACTION99.26
2.25-2.390.25751350.17442567X-RAY DIFFRACTION99.48
2.39-2.580.23491350.16842569X-RAY DIFFRACTION99.59
2.58-2.840.20931360.17532574X-RAY DIFFRACTION99.67
2.84-3.250.2491370.17712604X-RAY DIFFRACTION99.93
3.25-4.090.18891380.14712620X-RAY DIFFRACTION99.93
4.09-39.890.20611470.16872751X-RAY DIFFRACTION99.66
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)
13.51537210377-0.05032636737160.590886115873.262284574051.455541009558.323145851870.05801278666770.244288832377-0.126787155307-0.136596699259-0.0524614153879-0.2278375436960.2910182705530.211837779354-0.06097252042920.134572744681-0.01588945605530.02410070692190.1122394167230.01305137518450.17807668198422.053102627718.89276135947.93414494582
21.68692858067-0.08061244996840.4147169199842.14645178019-0.9965690898045.010516067330.00105273901735-0.2005919372920.02634298190090.3205103162920.00238120349899-0.00646230587003-0.121199569501-0.2735756599080.009764487537960.160845702175-0.01812590982540.005371991624610.117026701808-0.0215256877160.099688681785615.732838377629.672357767717.292372616
34.55245623416-0.7018250137841.226348739012.77759176841-0.5399122211674.56169062432-0.0214228007496-0.3448694828990.1532621408870.238917763578-0.0172079921167-0.307621162881-0.1550963311610.1393309100490.06228733857680.126852502801-0.01927323161530.008668504181330.120897716416-0.01823933649820.15851598940825.986705324128.412316407613.4263957194
43.6951123755-0.3652779395650.5046478201935.171424132652.547048543354.01776838515-0.1882121426050.09019825920420.1090936086950.1625148107370.336783358111-0.357299208609-0.06974513681880.451025010805-0.14037283050.122298353987-0.007432443341250.01306734658340.164788158038-0.002831713694850.24335664580532.541281346930.31175501911.5440185198
54.144176948790.1542049995231.306310240014.932247253674.298663656094.31053180078-0.215031524384-0.0543930135129-0.0111006854815-0.2429920867460.490185175179-0.782646669286-0.1340502546750.707662765949-0.1774453901590.192838361978-0.01654059783450.0464618308030.186443068937-0.04041277995050.48055072276629.470811886345.292455023215.8430199797
61.58625134428-0.590701164646-0.7758790377232.145532511670.9572056927965.24799273118-0.0525065744323-0.103297106588-0.02173621185390.1598278491770.0510641045209-0.09720057230570.181410601439-0.0624039159248-0.01026304852810.1349596872330.007474121026740.001295910401510.0829819994154-0.03250316087660.10937599046715.757128401639.276122973718.8098061982
73.91582970522-0.376862608951-3.046780410732.671525826210.3258932098982.514208254350.0154889081509-0.3411508721190.2764611450280.02604794265690.0458110280757-0.338638975335-0.5641334159540.346825693327-0.09463823322560.187203413334-0.0190233412151-0.02208836385970.140809895876-0.04347458607590.23933807210519.099453244848.745172123620.1468117332
81.99802520298-2.51438416156-2.532021184994.940632227224.234244392843.994362280230.1636240138570.1434558983130.310247019749-0.516118598477-0.0943018366312-0.0218384270037-0.494684757411-0.155437477519-0.07363841637830.2131760021420.02208614821470.009707002345330.1137780981080.001485327400050.20311671279612.037827873648.18857958510.9507094573
95.763806424130.611062649925-3.898935061443.95638223877-1.761646143418.85902760928-0.02389384024910.3321879822750.072739588603-0.04856942865780.007651627919520.09651462064330.106825758268-0.155209084009-0.03463659021210.111452761848-0.0394792197152-0.01486744308140.113333774735-0.02419542722250.1525511057438.6238930948424.08767105659.37395278131
103.0175003222-0.9666517750730.1245680788642.141536932730.01982251981640.8463832253390.0139677101687-0.0135660494882-0.1025701053070.121677898918-0.03563002315760.1491443917380.0258897143654-0.09373036336030.01101865761860.15344888664-0.0344048055734-0.01264993202060.1054091493270.02622017029720.0983314760247.7627802265915.233716641314.3365651542
114.510929740180.144364481073-4.21634368031.42042273796-0.585867783664.12352812448-0.172161090256-0.352216536265-0.4159159745510.06904653538770.05259257222650.04835688250450.281180424891-0.07084431054720.1248682687520.187562168480.00754456928698-0.0008389853331660.2574034131290.0559621135920.4029785320420.2714961593930.44551773578719.357931918
123.00664106486-0.01027325939561.807659950762.69217590139-1.08080017224.51484119270.0190749693959-0.489613270662-0.2480397484860.2064311800090.05703096024570.1270929210480.0148796194026-0.232985784818-0.08162513429330.1201899091590.01764306881880.04774932122810.1836012815330.0399889985560.18625676278814.15356291121.2629371568721.0088470689
132.70737782362-1.658980094232.590269479164.91164648524-4.958062548647.409476869160.1802753270370.0492700195721-0.335028259454-0.540896528463-0.282722507273-0.1777153301580.7165579773060.2835567201030.1116833373070.2379213791770.03722692693-0.01129138867870.139071563159-0.005337831567110.23275491157318.4908328379-4.4252095201112.3952846635
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 18 )AA0 - 181 - 19
22chain 'A' and (resid 19 through 51 )AA19 - 5120 - 52
33chain 'A' and (resid 52 through 70 )AA52 - 7053 - 71
44chain 'A' and (resid 71 through 96 )AA71 - 9672 - 97
55chain 'A' and (resid 97 through 112 )AA97 - 11298 - 113
66chain 'A' and (resid 113 through 139 )AA113 - 139114 - 140
77chain 'A' and (resid 140 through 157 )AA140 - 157141 - 158
88chain 'A' and (resid 158 through 179 )AA158 - 179159 - 180
99chain 'B' and (resid 1 through 18 )BD1 - 181 - 18
1010chain 'B' and (resid 19 through 88 )BD19 - 8819 - 88
1111chain 'B' and (resid 89 through 112 )BD89 - 11289 - 112
1212chain 'B' and (resid 113 through 157 )BD113 - 157113 - 157
1313chain 'B' and (resid 158 through 179 )BD158 - 179158 - 179

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