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- PDB-5fzt: The crystal structure of R7R8 in complex with a DLC1 fragment. -

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Basic information

Entry
Database: PDB / ID: 5fzt
TitleThe crystal structure of R7R8 in complex with a DLC1 fragment.
Components
  • RHO GTPASE-ACTIVATING PROTEIN 7
  • TALIN-1
KeywordsSTRUCTURAL PROTEIN / TALIN / DLC1 / FOCAL ADHESION
Function / homology
Function and homology information


hindbrain morphogenesis / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Platelet degranulation / negative regulation of focal adhesion assembly ...hindbrain morphogenesis / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Platelet degranulation / negative regulation of focal adhesion assembly / vinculin binding / integrin activation / regulation of Rho protein signal transduction / cell-substrate junction assembly / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / cortical actin cytoskeleton organization / RHOB GTPase cycle / cortical actin cytoskeleton / phosphatidylserine binding / RHOC GTPase cycle / RHOQ GTPase cycle / positive regulation of execution phase of apoptosis / CDC42 GTPase cycle / RHOA GTPase cycle / heart morphogenesis / positive regulation of protein dephosphorylation / forebrain development / ruffle / RAC1 GTPase cycle / SH2 domain binding / phosphatidylinositol binding / negative regulation of cell migration / GTPase activator activity / neural tube closure / caveola / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / adherens junction / structural constituent of cytoskeleton / ruffle membrane / platelet aggregation / cell-cell adhesion / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin filament binding / integrin binding / regulation of cell shape / actin cytoskeleton organization / cytoskeleton / membrane raft / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / focal adhesion / lipid binding / apoptotic process / cell surface / endoplasmic reticulum / signal transduction / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Talin, central domain / A middle domain of Talin 1 / : / Talin, R4 domain / in StAR and phosphatidylcholine transfer protein / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily ...Talin, central domain / A middle domain of Talin 1 / : / Talin, R4 domain / in StAR and phosphatidylcholine transfer protein / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / START domain / START domain / START domain profile. / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / FERM domain signature 2. / Rho GTPase activation protein / START-like domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / SAM domain (Sterile alpha motif) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MALONATE ION / Talin-1 / Rho GTPase-activating protein 7
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZacharchenko, T. / Qian, X. / Goult, B.T. / Jethwa, D. / Almeida, T. / Ballestrem, C. / Critchley, D.R. / Lowy, D.R. / Barsukov, I.L.
CitationJournal: Structure / Year: 2016
Title: Ld Motif Recognition by Talin: Structure of the Talin-Dlc1 Complex.
Authors: Zacharchenko, T. / Qian, X. / Goult, B.T. / Jethwa, D. / Almeida, T.B. / Ballestrem, C. / Critchley, D.R. / Lowy, D.R. / Barsukov, I.L.
History
DepositionMar 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Refinement description
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: 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: TALIN-1
B: RHO GTPASE-ACTIVATING PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5824
Polymers35,3782
Non-polymers2042
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-13.7 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.260, 73.260, 111.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

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Components

#1: Protein TALIN-1


Mass: 32574.725 Da / Num. of mol.: 1 / Fragment: R7R8, UNP RESIDUES 1359-1659 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / References: UniProt: P26039
#2: Protein/peptide RHO GTPASE-ACTIVATING PROTEIN 7 / DELETED IN LIVER CANCER 1 PROTEIN / DLC-1 / HP PROTEIN / RHO-TYPE GTPASE-ACTIVATING PROTEIN 7 / ...DELETED IN LIVER CANCER 1 PROTEIN / DLC-1 / HP PROTEIN / RHO-TYPE GTPASE-ACTIVATING PROTEIN 7 / START DOMAIN-CONTAINING PROTEIN 12 / STARD12 / STAR-RELATED LIPID TRANSFER PROTEIN 12 / DLC1


Mass: 2803.196 Da / Num. of mol.: 1 / Fragment: TBS, UNP RESIDUES 467-489 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q96QB1
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.45 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7.4 / Details: 15% ETHANOL, 0.1 M TRIS PH 7.4 AT 4OC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→55.18 Å / Num. obs: 20847 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 31.16 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.11
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10 (PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X0C

2x0c


Resolution: 2.1→55.181 Å / SU ML: 0.24 / σ(F): 1.37 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 1070 5.1 %
Rwork0.1766 --
obs0.1794 20847 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→55.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 14 165 2630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082505
X-RAY DIFFRACTIONf_angle_d0.8853394
X-RAY DIFFRACTIONf_dihedral_angle_d13.8531558
X-RAY DIFFRACTIONf_chiral_restr0.047391
X-RAY DIFFRACTIONf_plane_restr0.007456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.26441280.20342436X-RAY DIFFRACTION100
2.1956-2.31140.29271310.20332427X-RAY DIFFRACTION100
2.3114-2.45620.30771520.19552418X-RAY DIFFRACTION100
2.4562-2.64580.25591330.20372434X-RAY DIFFRACTION100
2.6458-2.91210.23581220.20682469X-RAY DIFFRACTION100
2.9121-3.33340.23961380.18722486X-RAY DIFFRACTION100
3.3334-4.19960.19751370.15312476X-RAY DIFFRACTION100
4.1996-55.20050.20091290.15572631X-RAY DIFFRACTION100
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)
12.0317-1.24140.87732.0122-0.14431.124-0.1105-0.15670.18980.25710.0572-0.3798-0.1770.01610.0570.334-0.0439-0.00990.17920.02190.2392-27.9553.54721.4865
20.9764-0.6243-0.09781.19080.46881.0552-0.0452-0.0656-0.0588-0.00520.00020.0666-0.097-0.08950.06920.1692-0.0781-0.01170.13830.04830.2144-39.50169.167534.7284
38.8309-1.61755.57472.8949-1.44473.6292-0.2956-0.12390.3490.26310.1733-0.0792-0.92260.24720.18090.1998-0.05480.00750.1684-0.010.2461-39.750824.895248.2213
41.9999-2.505823.5086-0.882.00013.5468-11.8014-1.26578.7322-5.79420.07875.3892-13.93192.24820.7717-0.1653-0.07251.28430.17650.675-49.208329.628728.7521
58.6728-4.04926.0103-7.15922-1.912417.2653-5.0734-2.53192.7019-8.8009-3.41898.822-0.79580.6514-0.14150.28561.07840.04621.2905-45.956228.102723.5573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1354:1466)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1467:1659)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 467:489)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1490)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1491)

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