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- PDB-1cjf: PROFILIN BINDS PROLINE-RICH LIGANDS IN TWO DISTINCT AMIDE BACKBON... -

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Basic information

Entry
Database: PDB / ID: 1cjf
TitlePROFILIN BINDS PROLINE-RICH LIGANDS IN TWO DISTINCT AMIDE BACKBONE ORIENTATIONS
Components
  • PROTEIN (HUMAN PLATELET PROFILIN)
  • PROTEIN (PROLINE PEPTIDE)
KeywordsSTRUCTURAL REGULATION PROTEIN / PROFILIN / ACTIN-BINDING PROTEIN / CYTOSKELETON / POLY-L-PROLINE
Function / homology
Function and homology information


synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / Signaling by ROBO receptors / positive regulation of ATP-dependent activity / proline-rich region binding ...synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / Signaling by ROBO receptors / positive regulation of ATP-dependent activity / proline-rich region binding / PCP/CE pathway / 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 / actin cytoskeleton organization / cell cortex / blood microparticle / cytoskeleton / protein stabilization / cadherin binding / focal adhesion / regulation of transcription by RNA polymerase II / glutamatergic synapse / RNA binding / extracellular exosome / nucleus / membrane / cytoplasm / cytosol
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
7-HYDROXY-4-METHYL-3-(2-HYDROXY-ETHYL)COUMARIN / Profilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMahoney, N.M. / Fedorov, A.A. / Fedorov, E. / Rozwarski, D.A. / Almo, S.C.
CitationJournal: 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.
History
DepositionApr 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN (HUMAN PLATELET PROFILIN)
C: PROTEIN (PROLINE PEPTIDE)
B: PROTEIN (HUMAN PLATELET PROFILIN)
D: PROTEIN (PROLINE PEPTIDE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2706
Polymers32,8304
Non-polymers4402
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.400, 51.800, 77.500
Angle α, β, γ (deg.)90.00, 131.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.066716, -0.003106, 0.997767), (-0.00346, -0.999988, -0.003345), (0.997766, -0.003675, 0.066704)
Vector: 58.8377, 33.4436, -49.5068)

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Components

#1: Protein PROTEIN (HUMAN PLATELET PROFILIN)


Mass: 14940.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HMC FLUOROPHORE / Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / References: UniProt: P07737
#2: Protein/peptide PROTEIN (PROLINE PEPTIDE)


Mass: 1474.737 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-HOM / 7-HYDROXY-4-METHYL-3-(2-HYDROXY-ETHYL)COUMARIN


Mass: 220.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: 1.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.1 M NACL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18.5 mg/mlprotein1drop
31.4 Mammonium sulfate1reservoir
40.1 MHEPES1reservoir
50.1 M1reservoirNaCl
2peptide1drop1:1.5 molar ratio

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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: Jul 1, 1998 / 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: 2.3→8 Å / Num. obs: 11957 / % possible obs: 90 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIL

1fil


Resolution: 2.3→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.293 -10 %RANDOM
Rwork0.195 ---
obs-11957 90 %-
Displacement parametersBiso mean: 22.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 32 24 2343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.39
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.729
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.729

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