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- PDB-3smz: Human raver1 RRM1-3 domains (residues 39-320) -

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Basic information

Entry
Database: PDB / ID: 3smz
TitleHuman raver1 RRM1-3 domains (residues 39-320)
ComponentsRibonucleoprotein PTB-binding 1
KeywordsRNA BINDING PROTEIN / RNA binding / ribonucleoprotein / RNA recognition motif / vinculin / alpha-actinin / nucleus
Function / homology
Function and homology information


RNA binding / nucleus / cytoplasm
Similarity search - Function
Ribonucleoprotein PTB-binding 1 / Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...Ribonucleoprotein PTB-binding 1 / Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonucleoprotein PTB-binding 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsRangarajan, E.S. / Lee, J.H. / Izard, T.
CitationJournal: Protein Sci. / Year: 2011
Title: Apo raver1 structure reveals distinct RRM domain orientations.
Authors: Rangarajan, E.S. / Lee, J.H. / Izard, T.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ribonucleoprotein PTB-binding 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7803
Polymers31,5881
Non-polymers1922
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.020, 104.020, 50.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ribonucleoprotein PTB-binding 1 / Protein raver-1


Mass: 31587.953 Da / Num. of mol.: 1 / Fragment: Tandem RRM domains (UNP residues 39-320)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1978, RAVER1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IY67
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris-HCl (pH 8.5), 24% PEG 3350, 200 mM Lithium sulfate, Vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→90.09 Å / Num. all: 21480 / Num. obs: 21054 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 41.87 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 29.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.99-2.14.10.5032.1190
6.31-90.096.90.01494.8199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.02 Å
Translation2.5 Å34.02 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
XDSdata reduction
BUSTER2.9.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H2U, chain B

3h2u


Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.9363 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: used TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 1051 5 %RANDOM
Rwork0.1853 ---
obs0.1877 21009 --
all-21033 --
Displacement parametersBiso mean: 57.38 Å2
Baniso -1Baniso -2Baniso -3
1--4.3112 Å20 Å20 Å2
2---4.3112 Å20 Å2
3---8.6225 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 10 235 2428
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012263HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053065HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1069SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes337HARMONIC5
X-RAY DIFFRACTIONt_it2263HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion2.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion281SEMIHARMONIC5
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_contact2610SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.09 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2381 115 4.87 %
Rwork0.2236 2245 -
all0.2243 2360 -
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)
11.574-1.82541.08892.7453-2.03762.1194-0.14080.04190.20050.3024-0.1329-0.2123-0.21860.40110.2736-0.09090.0399-0.0473-0.03870.0016-0.083619.86160.2618.209
25.51252.7872-2.61443.8977-1.29263.56360.05930.5360.3273-0.4637-0.0849-0.4395-0.28210.46560.0255-0.20120.0430.05560.10020.2076-0.141323.776278.1182-14.4566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|38 - A|220}A38 - 220
2X-RAY DIFFRACTION2{A|221 - A|316}A221 - 316

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