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- PDB-2d1x: The crystal structure of the cortactin-SH3 domain and AMAP1-pepti... -

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Basic information

Entry
Database: PDB / ID: 2d1x
TitleThe crystal structure of the cortactin-SH3 domain and AMAP1-peptide complex
Components
  • cortactin isoform a
  • proline rich region from development and differentiation enhancing factor 1
KeywordsCELL INVASION / SH3 / PROLINE-RICH / COMPLEX
Function / homology
Function and homology information


positive regulation of membrane tubulation / lamellipodium organization / mitotic spindle midzone / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / profilin binding / substrate-dependent cell migration, cell extension / positive regulation of smooth muscle contraction / regulation of autophagy of mitochondrion / protein localization to cilium ...positive regulation of membrane tubulation / lamellipodium organization / mitotic spindle midzone / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / profilin binding / substrate-dependent cell migration, cell extension / positive regulation of smooth muscle contraction / regulation of autophagy of mitochondrion / protein localization to cilium / focal adhesion assembly / podosome / regulation of axon extension / regulation of postsynapse organization / dendritic spine maintenance / phosphatidylserine binding / cortical cytoskeleton / positive regulation of actin filament polymerization / RHO GTPases activate PAKs / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / cilium assembly / voltage-gated potassium channel complex / extrinsic apoptotic signaling pathway / clathrin-coated pit / ruffle / phosphatidylinositol-4,5-bisphosphate binding / receptor-mediated endocytosis / GTPase activator activity / neuron projection morphogenesis / trans-Golgi network membrane / cell motility / negative regulation of extrinsic apoptotic signaling pathway / intracellular protein transport / lamellipodium / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / dendritic spine / cytoskeleton / cadherin binding / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ASAP1, BAR domain / ASAP1, SH3 domain / Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Arf GTPase activating protein ...ASAP1, BAR domain / ASAP1, SH3 domain / Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
: / Src substrate cortactin / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHashimoto, S. / Hirose, M. / Hashimoto, A. / Morishige, M. / Yamada, A. / Hosaka, H. / Akagi, K. / Ogawa, E. / Oneyama, C. / Agatsuma, T. ...Hashimoto, S. / Hirose, M. / Hashimoto, A. / Morishige, M. / Yamada, A. / Hosaka, H. / Akagi, K. / Ogawa, E. / Oneyama, C. / Agatsuma, T. / Okada, M. / Kobayashi, H. / Wada, H. / Nakano, H. / Ikegami, T. / Nakagawa, A. / Sabe, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Targeting AMAP1 and cortactin binding bearing an atypical src homology 3/proline interface for prevention of breast cancer invasion and metastasis.
Authors: Hashimoto, S. / Hirose, M. / Hashimoto, A. / Morishige, M. / Yamada, A. / Hosaka, H. / Akagi, K. / Ogawa, E. / Oneyama, C. / Agatsuma, T. / Okada, M. / Kobayashi, H. / Wada, H. / Nakano, H. ...Authors: Hashimoto, S. / Hirose, M. / Hashimoto, A. / Morishige, M. / Yamada, A. / Hosaka, H. / Akagi, K. / Ogawa, E. / Oneyama, C. / Agatsuma, T. / Okada, M. / Kobayashi, H. / Wada, H. / Nakano, H. / Ikegami, T. / Nakagawa, A. / Sabe, H.
History
DepositionSep 1, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: cortactin isoform a
B: cortactin isoform a
C: cortactin isoform a
D: cortactin isoform a
P: proline rich region from development and differentiation enhancing factor 1
Q: proline rich region from development and differentiation enhancing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9448
Polymers32,7526
Non-polymers1922
Water4,143230
1
A: cortactin isoform a
B: cortactin isoform a
P: proline rich region from development and differentiation enhancing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4724
Polymers16,3763
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: cortactin isoform a
D: cortactin isoform a
Q: proline rich region from development and differentiation enhancing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4724
Polymers16,3763
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.450, 132.140, 61.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
cortactin isoform a


Mass: 7345.027 Da / Num. of mol.: 4 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTTN(AMINO ACIDS 490-550) / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q14247
#2: Protein/peptide proline rich region from development and differentiation enhancing factor 1


Mass: 1686.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: GenBank: 46094081, UniProt: Q9ULH1*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: ammonium sulfate, sodium chloride, Hepes, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 12, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 23138 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3359 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 605405.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1164 5 %RANDOM
Rwork0.216 ---
obs0.216 23121 99.4 %-
all-345100 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9422 Å2 / ksol: 0.374901 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å20 Å20 Å2
2---7.24 Å20 Å2
3---10.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 10 230 2314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.912
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.492.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 204 5.3 %
Rwork0.309 3611 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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