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- PDB-3zv0: Structure of the SHQ1P-CBF5P complex -

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Basic information

Entry
Database: PDB / ID: 3zv0
TitleStructure of the SHQ1P-CBF5P complex
Components
  • H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 4
  • PROTEIN SHQ1
KeywordsCELL CYCLE / RNP ASSEMBLY / X-LINKED DYSKERATOSIS CONGENITA / TELOMERASE
Function / homology
Function and homology information


snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / rRNA modification / chromosome, centromeric region / 90S preribosome / rRNA processing / unfolded protein binding / microtubule / cell cycle / cell division / mRNA binding / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / tRNA pseudouridylate synthase B, C-terminal ...Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Uncharacterised domain CHP00451 / PUA domain / CS domain / CS domain profile. / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / HSP20-like chaperone / PUA-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
H/ACA ribonucleoprotein complex subunit CBF5 / Protein SHQ1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWalbott, H. / Machado-Pinilla, R. / Liger, D. / Blaud, M. / Rety, S. / Grozdanov, P.N. / Godin, K. / vanTilbeurgh, H. / Varani, G. / Meier, U.T. / Leulliot, N.
CitationJournal: Genes Dev. / Year: 2011
Title: The H/Aca Rnp Assembly Factor Shq1 Functions as an RNA Mimic.
Authors: Walbott, H. / Machado-Pinilla, R. / Liger, D. / Blaud, M. / Rety, S. / Grozdanov, P.N. / Godin, K. / Van Tilbeurgh, H. / Varani, G. / Meier, U.T. / Leulliot, N.
History
DepositionJul 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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: PROTEIN SHQ1
B: PROTEIN SHQ1
C: H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 4
D: H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1709
Polymers130,7104
Non-polymers4605
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-62.4 kcal/mol
Surface area42620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.060, 154.060, 121.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96577, -0.25451, -0.05012), (-0.25211, 0.8755, 0.41224), (-0.06104, 0.41076, -0.9097)68.62132, -7.8343, 74.35788
2given(-0.97125, -0.2342, -0.04265), (-0.23087, 0.88309, 0.40846), (-0.058, 0.40657, -0.91178)69.62764, -7.6589, 74.14545

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Components

#1: Protein PROTEIN SHQ1 / SHQ1P / SMALL NUCLEOLAR RNAS OF THE BOX H/ACA FAMILY QUANTITATIVE ACCUMULATION PROTEIN 1


Mass: 43503.730 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 145-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: P40486
#2: Protein H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 4 / CENTROMERE-BINDING FACTOR 5 / CENTROMERE/MICROTUBULE-BINDING PROTEIN CBF5 / H/ACA SNORNP PROTEIN ...CENTROMERE-BINDING FACTOR 5 / CENTROMERE/MICROTUBULE-BINDING PROTEIN CBF5 / H/ACA SNORNP PROTEIN CBF5 / SMALL NUCLEOLAR RNP PROTEIN CBF5 / P64' / CBF5P


Mass: 21851.266 Da / Num. of mol.: 2 / Fragment: DCAT DOMAIN, RESIDUES 1-60,258-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS
References: UniProt: P33322, Isomerases; Intramolecular transferases; Transferring other groups
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.24 Å3/Da / Density % sol: 62.08 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: CRYSTALLIZED AT 291 KELVIN BY THE HANGING DROP VAPOR DIFFUSION METHOD FROM A 1:1 UL OF PROTEIN AND PRECIPITANT CONTAINING 4 TO 8 % PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 36623 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 66.7 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.21 Å / Cor.coef. Fo:Fc: 0.9284 / Cor.coef. Fo:Fc free: 0.9095 / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHAINS A, B, RESIDUES 145-164 DISORDERED. CHAINS C, D, RESIDUES 6XHISTAG, 1-18, 43-46, 378-386 ARE DISORDERED. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1830 5 %RANDOM
Rwork0.1782 ---
obs0.1797 36596 --
Displacement parametersBiso mean: 59.79 Å2
Baniso -1Baniso -2Baniso -3
1-7.9918 Å20 Å20 Å2
2--7.9918 Å20 Å2
3----15.9836 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7849 0 30 99 7978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098029HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0410839HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2895SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes231HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1111HARMONIC5
X-RAY DIFFRACTIONt_it8029HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion18.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1036SEMIHARMONIC5
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_contact8932SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2621 150 5.1 %
Rwork0.2183 2791 -
all0.2206 2941 -
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)
12.8867-0.45730.53441.66780.01511.570.02540.136-0.3002-0.04340.00890.29680.0862-0.1401-0.0343-0.191-0.04060.0091-0.1372-0.0629-0.095611.1623-42.49224.0724
22.35660.2416-0.13781.62580.18261.7407-0.0103-0.3612-0.24170.13960.0706-0.32360.16040.1883-0.0604-0.22260.0388-0.0461-0.16880.0502-0.043367.4466-37.972333.9795
32.94050.72720.02671.7401-0.59791.40280.0728-0.3118-0.0380.1485-0.10240.1365-0.08880.04050.0296-0.1391-0.02810.0039-0.12320.0127-0.217327.5201-35.193636.9868
42.59330.2494-0.55740.6750.18051.3942-0.04320.13420.1343-0.00320.046-0.1052-0.0095-0.1494-0.0028-0.1141-0.046-0.0108-0.08770.0224-0.105748.8257-30.092225.7774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 165:346, 362:504)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 165:346, 361:507)
3X-RAY DIFFRACTION3CHAIN C AND (RESID 20:37, 47:60, 258:377)
4X-RAY DIFFRACTION4CHAIN D AND (RESID 19:42, 48:60, 258:377)

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