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- PDB-2v3m: Structure of the Gar1 domain of NAf1 -

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Basic information

Entry
Database: PDB / ID: 2v3m
TitleStructure of the Gar1 domain of NAf1
ComponentsNAF1
KeywordsRIBOSOMAL PROTEIN / NAF1 / GAR1 / SNORNP / PHOSPHORYLATION / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


box H/ACA snoRNP assembly / pseudouridine synthesis / sno(s)RNA-containing ribonucleoprotein complex / rRNA processing / ribosome biogenesis / RNA binding / nucleoplasm / nucleus
Similarity search - Function
H/ACA ribonucleoprotein complex non-core subunit Naf1 / Probable tRNA pseudouridine synthase domain / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
H/ACA ribonucleoprotein complex non-core subunit NAF1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsLeulliot, N. / Godin, K.S. / Hoareau-Aveilla, C. / Quevillon-Cheruel, S. / Varani, G. / Henry, Y. / van Tilbeurgh, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Box H/Aca Rnp Assembly Factor Naf1P Contains a Domain Homologous to Gar1P Mediating its Interaction with Cbf5P.
Authors: Leulliot, N. / Godin, K.S. / Hoareau-Aveilla, C. / Quevillon-Cheruel, S. / Varani, G. / Henry, Y. / Van Tilbeurgh, H.
History
DepositionJun 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: NAF1
B: NAF1
C: NAF1
D: NAF1
E: NAF1
F: NAF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,07713
Polymers91,4056
Non-polymers6727
Water00
1
A: NAF1
F: NAF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6604
Polymers30,4682
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-35.4 kcal/mol
Surface area10750 Å2
MethodPISA
2
C: NAF1
D: NAF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7565
Polymers30,4682
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-48.6 kcal/mol
Surface area11160 Å2
MethodPISA
3
B: NAF1
E: NAF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6604
Polymers30,4682
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-34.6 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.534, 103.534, 109.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31A
41F
51E
61D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B124 - 153
2111C124 - 153
3111A124 - 153
4111F124 - 153
5111E124 - 153
6111D124 - 153
1211B168 - 221
2211C168 - 221
3211A168 - 221
4211F168 - 221
5211E168 - 221
6211D168 - 221

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Components

#1: Protein
NAF1 / HYPOTHETICAL 54.9 KDA PROTEIN IN SPC98-TOM70 INTERGENIC REGION


Mass: 15234.103 Da / Num. of mol.: 6 / Fragment: RESIDUES 109-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD (DE3), / References: UniProt: P53919
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 33.9 %
Crystal growpH: 5.6
Details: 2M AMMONIUM SULPHATE, 0.2M K/NA TARTRATE, NA CITRATE PH5.6., pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.74→20 Å / Num. obs: 18030 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.9
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SHELXDphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD / Resolution: 2.74→19.57 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.897 / SU B: 36.644 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 914 5.1 %RANDOM
Rwork0.257 ---
obs0.259 17085 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.45 Å20 Å2
2--0.89 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.74→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 35 0 4576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0224648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6342.0116276
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55725.026193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.17215890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8471521
X-RAY DIFFRACTIONr_chiral_restr0.1440.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023329
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.21944
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3450.23306
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4230.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7671.52873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27724638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84431905
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0444.51638
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 670 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Btight positional0.230.05
2Ctight positional0.280.05
3Atight positional0.310.05
4Ftight positional0.320.05
5Etight positional0.230.05
6Dtight positional0.310.05
1Btight thermal0.420.5
2Ctight thermal0.610.5
3Atight thermal0.820.5
4Ftight thermal0.490.5
5Etight thermal1.020.5
6Dtight thermal0.490.5
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 73
Rwork0.341 1220

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