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- PDB-9zrd: Crystal structure of macrodomain from Eastern Equine Encephalitis... -

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Basic information

Entry
Database: PDB / ID: 9zrd
TitleCrystal structure of macrodomain from Eastern Equine Encephalitis Virus in complex with Adenosine diphosphate ribose
ComponentsPolyprotein P1234
KeywordsVIRAL PROTEIN / MACRO DOMAIN / alpha virus / Adenosine diphosphate ribose
Function / homology
Function and homology information


host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity ...host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / methylation / RNA helicase activity / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / host cell nucleus / GTP binding / host cell plasma membrane / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain ...Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Viral superfamily 1 RNA helicase core domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Chem-AR6 / Polyprotein P1234
Similarity search - Component
Biological speciesEastern equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsChang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Crystal structure of macrodomain from Eastern Equine Encephalitis Virus in complex with Adenosine diphosphate ribose
Authors: Chang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.
History
DepositionDec 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5244
Polymers17,3101
Non-polymers1,2153
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.925, 47.462, 66.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyprotein P1234 / Non-structural polyprotein


Mass: 17309.582 Da / Num. of mol.: 1 / Fragment: Macrodomain, residues 1327-1481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66580
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 1.82 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Bis-Tris pH 5.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 13670 / % possible obs: 92.9 % / Redundancy: 7 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.919 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7330.4464410.8570.9610.2550.5190.72661.4
1.73-1.763.50.3575400.9040.9750.1810.4030.74475.5
1.76-1.794.10.426440.880.9680.2080.4710.69489.8
1.79-1.834.80.4146930.910.9760.1920.4580.7494.4
1.83-1.875.60.3766750.9440.9860.1660.4130.75997.1
1.87-1.916.70.3477490.9810.9950.1410.3750.79199.6
1.91-1.967.70.3327030.9880.9970.1290.3560.861100
1.96-2.028.20.37390.9790.9950.1120.3210.908100
2.02-2.078.60.2487200.9850.9960.0910.2650.902100
2.07-2.148.70.2087190.9860.9960.0760.2220.96299.6
2.14-2.228.50.1727310.9910.9980.0640.1841.01899.7
2.22-2.318.30.1547090.990.9970.0570.1651.03199.4
2.31-2.417.70.1287460.9910.9980.050.1381.03399.6
2.41-2.548.20.1117200.990.9980.0420.1191.0398.6
2.54-2.77.80.0917180.9930.9980.0360.0981.01497.8
2.7-2.918.10.0787120.9940.9990.0310.0840.9895.4
2.91-3.27.60.0636770.9960.9990.0260.0690.92892
3.2-3.666.70.0536530.9960.9990.0230.0580.95985.5
3.66-4.6160.0466190.9940.9990.0210.0510.89881.3
4.61-506.50.0447620.9960.9990.0190.0480.77691

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→38.62 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 600 4.87 %
Rwork0.1723 --
obs0.1746 12327 84.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 41 103 1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061327
X-RAY DIFFRACTIONf_angle_d0.7761815
X-RAY DIFFRACTIONf_dihedral_angle_d13.5522
X-RAY DIFFRACTIONf_chiral_restr0.057207
X-RAY DIFFRACTIONf_plane_restr0.005227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.860.2776870.23081791X-RAY DIFFRACTION52
1.86-2.130.23181720.17783299X-RAY DIFFRACTION96
2.13-2.690.20561690.17493430X-RAY DIFFRACTION99
2.69-38.620.2111720.16043207X-RAY DIFFRACTION89
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)
11.71890.5715-0.49953.1788-2.41772.99570.06690.00330.06580.0573-0.2154-0.272-0.06880.25520.24080.09930.0546-0.03690.18950.04820.197317.08173.040414.8705
21.7359-0.22420.68181.7843-0.41362.6938-0.0313-0.1004-0.08660.0590.00120.16330.0756-0.08150.00350.09050.00880.0340.10820.00730.11470.32632.832712.6891
31.0012-0.54710.1020.92750.1711.9546-0.1179-0.0114-0.15370.03020.08160.22090.0241-0.178-0.02010.1046-0.0040.01340.1060.01130.1448-5.13853.327610.4956
40.9803-0.7232-0.66821.63930.98071.8008-0.09420.1027-0.0507-0.0756-0.05150.07020.1153-0.16040.06970.1201-0.01040.02570.0957-0.00840.0958-0.63373.88574.9295
50.5347-0.1499-0.17524.1992.63552.59220.00180.12970.0742-0.247-0.03360.0824-0.0553-0.04520.05290.14110.01760.06580.15070.02430.1137.0146.479-1.3595
61.92160.50950.17074.14970.55131.99350.023-0.030.20750.102-0.0241-0.1307-0.01920.0307-0.01950.0895-0.01320.01340.14230.00740.13258.925611.164512.0796
70.74160.0442-0.37120.273-0.07980.4713-0.0611-0.0109-0.0754-0.0647-0.016-0.09360.19750.104-0.06280.15570.06310.07640.12530.01010.127711.2134-2.29492.6985
81.7319-0.3356-0.16291.8172-1.33462.97650.0026-0.0732-0.08330.1084-0.0365-0.2505-0.04030.23170.050.06370.02670.00840.13630.02960.104313.05083.93613.0566
93.2066-0.00480.61341.3642-0.28251.46030.05330.0387-0.24110.0062-0.0187-0.23290.11830.12410.00970.28350.19530.03520.37110.0840.363919.1561-6.193711.9222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 98 )
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 144 )
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 155 )

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