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- PDB-1cf0: HUMAN PLATELET PROFILIN COMPLEXED WITH AN L-PRO10-IODOTYROSINE PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1cf0
TitleHUMAN PLATELET PROFILIN COMPLEXED WITH AN L-PRO10-IODOTYROSINE PEPTIDE
Components
  • PROTEIN (L-PRO10-IODOTYROSINE)
  • PROTEIN (PROFILIN)
KeywordsCOMPLEX (ACTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (ACTIN-BINDING PROTEIN-PEPTIDE) / PROFILIN / POLY-L-PROLINE / ACTIN CYTOSKELETON / COMPLEX (ACTIN-BINDING PROTEIN-PEPTIDE) complex
Function / homology
Function and homology information


synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway ...synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / neural tube closure / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Platelet degranulation / actin binding / cell cortex / actin cytoskeleton organization / blood microparticle / protein stabilization / cytoskeleton / cadherin binding / focal adhesion / glutamatergic synapse / regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase ...Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.2 Å
AuthorsRozwarski, D.A. / Mahoney, N.M. / Almo, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Profilin binds proline-rich ligands in two distinct amide backbone orientations.
Authors: Mahoney, N.M. / Rozwarski, D.A. / Fedorov, E. / Fedorov, A.A. / Almo, S.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of the Profilin-Poly-L-Proline Complex Involved in Morphogenesis and Cytoskeletal Regulation
Authors: Mahoney, N.M. / Janmey, P.A. / Almo, S.C.
History
DepositionMar 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PROFILIN)
B: PROTEIN (PROFILIN)
C: PROTEIN (L-PRO10-IODOTYROSINE)


Theoretical massNumber of molelcules
Total (without water)30,8223
Polymers30,8223
Non-polymers00
Water70339
1
A: PROTEIN (PROFILIN)
C: PROTEIN (L-PRO10-IODOTYROSINE)


Theoretical massNumber of molelcules
Total (without water)15,9532
Polymers15,9532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PROFILIN)


Theoretical massNumber of molelcules
Total (without water)14,8691
Polymers14,8691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.290, 97.650, 38.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.935788, 0.199092, 0.29097), (0.347764, 0.656963, 0.668924), (-0.057979, 0.72716, -0.684015)
Vector: 32.151, -22.7846, 4.5604)

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Components

#1: Protein PROTEIN (PROFILIN)


Mass: 14868.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PLATELET / Description: SYNTHETIC / Cellular location: CYTOPLASM / Plasmid: PMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07737
#2: Protein/peptide PROTEIN (L-PRO10-IODOTYROSINE)


Mass: 1084.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The sequence occurs naturally in human
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE 11 OF CHAIN E REPRESENTS AN IODOTYROSINE RESIDUE CONNECTED BY A PEPTIDE BOND TO THE POLY- ...RESIDUE 11 OF CHAIN E REPRESENTS AN IODOTYROSINE RESIDUE CONNECTED BY A PEPTIDE BOND TO THE POLY-PROLINE-PEPTIDE LIGAND

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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: 42 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: other / Details: Mahoney, N.M., (1997) Nat.Struct.Biol., 4, 953.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 17247 / % possible obs: 95.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.62 / Rsym value: 0.62
Reflection
*PLUS
Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: WATER MOLECULES 201 - 214 INTERACT WITH PROTEIN CHAIN A WATER MOLECULES 301 - 314 INTERACT WITH PROTEIN CHAIN B AND EACH SET OF WATER MOLECULES ARE RELATED BY THE SAME NCS SYMMETRY THAT ...Details: WATER MOLECULES 201 - 214 INTERACT WITH PROTEIN CHAIN A WATER MOLECULES 301 - 314 INTERACT WITH PROTEIN CHAIN B AND EACH SET OF WATER MOLECULES ARE RELATED BY THE SAME NCS SYMMETRY THAT RELATES THE TWO PROTEIN CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1160 10 %RANDOM
Rwork0.21 ---
obs-12069 89.5 %-
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.122 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.214 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 0 39 2191
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.823
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.03
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.352
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.52.6
X-RAY DIFFRACTIONx_mcangle_it24.1
X-RAY DIFFRACTIONx_scbond_it24.1
X-RAY DIFFRACTIONx_scangle_it2.56.1
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 92 10 %
Rwork0.336 1081 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.03
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.352
LS refinement shell
*PLUS
Rfactor Rfree: 0.398 / Rfactor Rwork: 0.336

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