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- PDB-3vf0: Raver1 in complex with metavinculin L954 deletion mutant -

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Basic information

Entry
Database: PDB / ID: 3vf0
TitleRaver1 in complex with metavinculin L954 deletion mutant
Components
  • Ribonucleoprotein PTB-binding 1
  • Vinculin
KeywordsCELL ADHESION/PROTEIN BINDING / cytoskeletal F-actin binding protein / ribonucleoprotein / CELL ADHESION-PROTEIN BINDING complex
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 / terminal web / cell-substrate junction / 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 / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / negative regulation of cell migration / cell-matrix adhesion / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / specific granule lumen / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / Signaling by ALK fusions and activated point mutants / 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 / cytoplasm / cytosol
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 / Ribonucleoprotein PTB-binding 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsLee, J.H. / Vonrhein, C. / Bricogne, G. / Izard, T.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Metavinculin Tail Domain Directs Constitutive Interactions with Raver1 and vinculin RNA.
Authors: Lee, J.H. / Rangarajan, E.S. / Vonrhein, C. / Bricogne, G. / Izard, T.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vinculin
B: Ribonucleoprotein PTB-binding 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20516
Polymers62,7702
Non-polymers1,43614
Water4,576254
1
B: Ribonucleoprotein PTB-binding 1
hetero molecules

A: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20516
Polymers62,7702
Non-polymers1,43614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_664-x+1,-y+1,z-1/21
Buried area5910 Å2
ΔGint-5 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.905, 164.905, 102.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS A HETERODIMER.

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Components

#1: Protein Vinculin / Metavinculin


Mass: 31124.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P18206
#2: Protein Ribonucleoprotein PTB-binding 1 / Protein raver-1


Mass: 31645.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1978, RAVER1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8IY67
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.21 Å3/Da / Density % sol: 61.65 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→35.7 Å / Num. obs: 27610 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 55.75 Å2

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Processing

SoftwareName: BUSTER / Version: 2.13.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→35.7 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9296 / SU R Cruickshank DPI: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1390 5.03 %RANDOM
Rwork0.1683 ---
obs0.1701 27610 99.99 %-
Displacement parametersBiso mean: 45.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.0974 Å20 Å20 Å2
2---2.0974 Å20 Å2
3---4.1948 Å2
Refine analyzeLuzzati coordinate error obs: 0.261 Å
Refinement stepCycle: LAST / Resolution: 2.54→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 93 254 3931
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013739HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065030HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1798SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes533HARMONIC5
X-RAY DIFFRACTIONt_it3739HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion18.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion487SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle2HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4435SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.64 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2367 152 5.32 %
Rwork0.1774 2703 -
all0.1805 2855 -
obs--99.99 %
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)
12.1979-0.1652-0.63911.0363-0.1681.0838-0.00250.1049-0.0524-0.0156-0.0652-0.07270.12840.01250.06760.01460.0552-0.0262-0.1075-0.0104-0.111955.152250.411-4.6739
20.1028-0.08650.02480.7794-0.38951.3101-0.00370.024-0.07420.07790.011-0.0153-0.15850.2344-0.0073-0.0817-0.0242-0.021-0.0183-0.0001-0.04462.993683.9507-39.2555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A956 - 1133
2X-RAY DIFFRACTION2B37 - 319

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