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- PDB-1vec: Crystal structure of the N-terminal domain of rck/p54, a human DE... -

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Basic information

Entry
Database: PDB / ID: 1vec
TitleCrystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein
ComponentsATP-dependent RNA helicase p54
KeywordsRNA BINDING PROTEIN / RNA HELICASE / DEAD-BOX PROTEIN
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / RISC complex / P-body assembly / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body ...mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / RISC complex / P-body assembly / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Probable ATP-dependent RNA helicase DDX6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHogetsu, K. / Matsui, T. / Yukihiro, Y. / Tanaka, M. / Sato, T. / Kumasaka, T. / Tanaka, N.
CitationJournal: Genes Cells / Year: 2006
Title: Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes
Authors: Matsui, T. / Hogetsu, K. / Usukura, J. / Sato, T. / Kumasaka, T. / Akao, Y. / Tanaka, N.
History
DepositionMar 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase p54
B: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4424
Polymers46,2262
Non-polymers2152
Water5,855325
1
A: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1782
Polymers23,1131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2632
Polymers23,1131
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ATP-dependent RNA helicase p54
hetero molecules

B: ATP-dependent RNA helicase p54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4424
Polymers46,2262
Non-polymers2152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1210 Å2
ΔGint-34 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.520, 73.140, 84.790
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 ATP-dependent RNA helicase p54 / RCK / DEAD-box protein 6


Mass: 23113.076 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMRCK / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P26196
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG3350, di-sodium tartrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→29.9 Å / Num. all: 52406 / Num. obs: 52054 / % possible obs: 99.3 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.4
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5271 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QDE

1qde


Resolution: 2.01→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 116477.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2534 4.9 %RANDOM
Rwork0.198 ---
all0.198 ---
obs0.198 51717 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4738 Å2 / ksol: 0.335418 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--3.08 Å20 Å2
3----3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.01→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 11 325 3568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 366 4.7 %
Rwork0.284 7477 -
obs-7477 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TAR_XPLOR_PARAMTAR_XPLOR_TOP

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