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- PDB-4cc3: Complex of human Tuba C-terminal SH3 domain and Mena proline-rich... -

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Basic information

Entry
Database: PDB / ID: 4cc3
TitleComplex of human Tuba C-terminal SH3 domain and Mena proline-rich peptide - H3
Components
  • DYNAMIN-BINDING PROTEIN
  • PROTEIN ENABLED HOMOLOG
KeywordsSTRUCTURAL PROTEIN / TUBA / SRC HOMOLOGY 3 / SH3 DOMAIN / MENA / NDPP-1 / PROLINE- RICH PEPTIDE / ACTIN CYTOSKELETON / CORTICAL TENSION
Function / homology
Function and homology information


Signaling by ROBO receptors / actin polymerization-dependent cell motility / profilin binding / actin polymerization or depolymerization / Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / stress fiber / axon guidance ...Signaling by ROBO receptors / actin polymerization-dependent cell motility / profilin binding / actin polymerization or depolymerization / Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / stress fiber / axon guidance / actin filament organization / guanyl-nucleotide exchange factor activity / cellular response to leukemia inhibitory factor / neural tube closure / filopodium / SH3 domain binding / cell-cell junction / presynapse / regulation of cell shape / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cytoskeleton / neuron projection / intracellular signal transduction / nuclear body / focal adhesion / synapse / nucleolus / Golgi apparatus / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / : / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / BAR domain / BAR domain profile. ...Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / : / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / BAR domain / BAR domain profile. / BAR / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / BAR domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / AH/BAR domain superfamily / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein enabled homolog / Dynamin-binding protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPolle, L. / Rigano, L. / Julian, R. / Ireton, K. / Schubert, W.-D.
CitationJournal: Structure / Year: 2014
Title: Structural Details of Human Tuba Recruitment by Inlc of Listeria Monocytogenes Elucidate Bacterial Cell-Cell Spreading.
Authors: Polle, L. / Rigano, L.A. / Julian, R. / Ireton, K. / Schubert, W.
History
DepositionOct 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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: DYNAMIN-BINDING PROTEIN
B: PROTEIN ENABLED HOMOLOG
C: DYNAMIN-BINDING PROTEIN
D: PROTEIN ENABLED HOMOLOG
E: DYNAMIN-BINDING PROTEIN
F: PROTEIN ENABLED HOMOLOG
G: DYNAMIN-BINDING PROTEIN
H: PROTEIN ENABLED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,96512
Polymers35,5048
Non-polymers4614
Water2,666148
1
A: DYNAMIN-BINDING PROTEIN
B: PROTEIN ENABLED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9113
Polymers8,8762
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-15.8 kcal/mol
Surface area4540 Å2
MethodPISA
2
C: DYNAMIN-BINDING PROTEIN
D: PROTEIN ENABLED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2664
Polymers8,8762
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-14.7 kcal/mol
Surface area4750 Å2
MethodPISA
3
E: DYNAMIN-BINDING PROTEIN
F: PROTEIN ENABLED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9113
Polymers8,8762
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-19.5 kcal/mol
Surface area4540 Å2
MethodPISA
4
G: DYNAMIN-BINDING PROTEIN
H: PROTEIN ENABLED HOMOLOG


Theoretical massNumber of molelcules
Total (without water)8,8762
Polymers8,8762
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9.1 kcal/mol
Surface area4840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.870, 115.870, 73.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
DYNAMIN-BINDING PROTEIN / SCAFFOLD PROTEIN TUBA


Mass: 7712.617 Da / Num. of mol.: 4 / Fragment: C-TERMINAL SH3 DOMAIN, RESIDUES 1513-1577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: Q6XZF7
#2: Protein/peptide
PROTEIN ENABLED HOMOLOG / NPC-DERIVED PROLINE-RICH PROTEIN 1 / NDPP-1 / MURINE MENA


Mass: 1163.321 Da / Num. of mol.: 4 / Fragment: PROLINE-RICH PEPTIDE, RESIDUES 547-558 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q03173
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST TWO RESIDUES OF THE SEQUENCE GP ARE REMNANTS OF THE FUSION PROTEIN CLEAVAGE

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 5.5 / Details: 2.5 M NACL, 0.1 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 25648 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUU

1zuu


Resolution: 1.97→34.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.721 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21508 1282 5 %RANDOM
Rwork0.18084 ---
obs0.1826 24356 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.781 Å2
Baniso -1Baniso -2Baniso -3
1--23.1 Å20 Å20 Å2
2---23.1 Å20 Å2
3---46.21 Å2
Refinement stepCycle: LAST / Resolution: 1.97→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 10 148 2513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022503
X-RAY DIFFRACTIONr_bond_other_d0.010.022363
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9633419
X-RAY DIFFRACTIONr_angle_other_deg1.88435471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23924.825114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60315393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.294159
X-RAY DIFFRACTIONr_chiral_restr0.1740.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212835
X-RAY DIFFRACTIONr_gen_planes_other0.010.02574
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 88 -
Rwork0.251 1673 -
obs--94.07 %
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)
13.76640.7481-0.03945.381-0.4851.76220.1688-0.02950.35340.2732-0.09960.5504-0.12010.004-0.06920.2336-0.00010.02920.21080.02720.085111.272-25.4715.195
22.83390.41960.73894.4340.2621.68590.1703-0.27150.05680.436-0.128-0.3189-0.1730.0118-0.04240.2943-0.045-0.01480.1828-0.00380.027224.293-7.73510.446
33.0999-1.14440.19113.4409-0.96572.14480.00140.25410.3062-0.2688-0.2239-0.51960.06430.16470.22250.2419-0.00180.07930.18640.01930.101824.5163.488-8.098
42.6216-1.2255-0.32164.32-1.05411.9450.11770.24160.0064-0.4349-0.25-0.27140.154-0.05970.13220.2181-0.0110.04410.20130.02430.024211.61919.809-15.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1514 - 1577
2X-RAY DIFFRACTION1B1 - 12
3X-RAY DIFFRACTION2C1514 - 1577
4X-RAY DIFFRACTION2D1 - 12
5X-RAY DIFFRACTION3E1514 - 1577
6X-RAY DIFFRACTION3F1 - 12
7X-RAY DIFFRACTION4G1514 - 1577
8X-RAY DIFFRACTION4H1 - 12

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