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- PDB-3h2u: Human raver1 RRM1, RRM2, and RRM3 domains in complex with human v... -

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Basic information

Entry
Database: PDB / ID: 3h2u
TitleHuman raver1 RRM1, RRM2, and RRM3 domains in complex with human vinculin tail domain Vt
Components
  • Raver-1
  • Vinculin
KeywordsCELL ADHESION / focal adhesion / actin cytoskeleton / RNP motif / RNA binding / Alternative splicing / Cytoplasm / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / podosome / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / beta-catenin binding / specific granule lumen / extracellular vesicle / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / cell-cell junction / Signaling by BRAF and RAF1 fusions / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribonucleoprotein PTB-binding 1 / Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily ...Ribonucleoprotein PTB-binding 1 / Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / RRM (RNA recognition motif) domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vinculin / Vinculin / Ribonucleoprotein PTB-binding 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLee, J.H. / Rangarajan, E.S. / Yogesha, S.D. / Izard, T.
CitationJournal: Structure / Year: 2009
Title: Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions
Authors: Lee, J.H. / Rangarajan, E.S. / Yogesha, S.D. / Izard, T.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
B: Raver-1
C: Vinculin
D: Raver-1


Theoretical massNumber of molelcules
Total (without water)105,1964
Polymers105,1964
Non-polymers00
Water73941
1
A: Vinculin
B: Raver-1


Theoretical massNumber of molelcules
Total (without water)52,5982
Polymers52,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vinculin
D: Raver-1


Theoretical massNumber of molelcules
Total (without water)52,5982
Polymers52,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.754, 94.906, 186.027
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 Vinculin /


Mass: 21222.484 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DTM7, UniProt: P18206*PLUS
#2: Protein Raver-1 / Ribonucleoprotein PTB-binding 1


Mass: 31375.662 Da / Num. of mol.: 2 / Fragment: RRM 1, RRM 2, and RRM 3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAVER1, KIAA1978 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IY67
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris (pH 7.5), 200 mM sodium nitrate, and 16% PEG-3,350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 40684 / Biso Wilson estimate: 77.504 Å2

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Processing

SoftwareName: BUSTER-TNT / Version: 1.3.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RKE

1rke


Resolution: 2.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 2024 5 %RANDOM
Rwork0.2245 ---
obs0.227 40500 99.65 %-
Displacement parametersBiso mean: 63.91 Å2
Baniso -1Baniso -2Baniso -3
1--8.84641202 Å20 Å20 Å2
2---6.46321735 Å20 Å2
3---15.30962937 Å2
Refine analyzeLuzzati coordinate error obs: 0.4835 Å
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 0 41 7167
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01172342
X-RAY DIFFRACTIONt_angle_deg1.33597142
X-RAY DIFFRACTIONt_dihedral_angle_d26.78815610
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0081942
X-RAY DIFFRACTIONt_gen_planes0.01610475
X-RAY DIFFRACTIONt_it1.844723420
X-RAY DIFFRACTIONt_nbd0.0531925
LS refinement shellResolution: 2.75→2.92 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2894 332 5.22 %
Rwork0.2701 6031 -
all0.2711 6363 -
obs--99.65 %

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