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- PDB-4b1v: Structure of the Phactr1 RPEL-N domain bound to G-actin -

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Basic information

Entry
Database: PDB / ID: 4b1v
TitleStructure of the Phactr1 RPEL-N domain bound to G-actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • PHOSPHATASE AND ACTIN REGULATOR 1
KeywordsSTRUCTURAL PROTEIN / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION / MUSCLE PROTEIN / ATP-BINDING / CYTOSKELETON
Function / homology
Function and homology information


dendrite arborization / regulation of neuron migration / protein phosphatase 1 binding / regulation of phosphorylation / actomyosin structure organization / protein phosphatase inhibitor activity / cytoskeletal motor activator activity / stress fiber assembly / tropomyosin binding / mesenchyme migration ...dendrite arborization / regulation of neuron migration / protein phosphatase 1 binding / regulation of phosphorylation / actomyosin structure organization / protein phosphatase inhibitor activity / cytoskeletal motor activator activity / stress fiber assembly / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cerebral cortex development / calcium-dependent protein binding / lamellipodium / actin binding / cell body / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / synapse / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. ...RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Phosphatase and actin regulator 1 / Actin, alpha skeletal muscle / Phosphatase and actin regulator 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMouilleron, S. / Wiezlak, M. / O'Reilly, N. / Treisman, R. / McDonald, N.Q.
CitationJournal: Structure / Year: 2012
Title: Structures of the Phactr1 RPEL domain and RPEL motif complexes with G-actin reveal the molecular basis for actin binding cooperativity.
Authors: Mouilleron, S. / Wiezlak, M. / O'Reilly, N. / Treisman, R. / McDonald, N.Q.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Feb 28, 2018Group: Advisory / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: ACTIN, ALPHA SKELETAL MUSCLE
B: ACTIN, ALPHA SKELETAL MUSCLE
M: PHOSPHATASE AND ACTIN REGULATOR 1
N: PHOSPHATASE AND ACTIN REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,90316
Polymers91,6164
Non-polymers2,28612
Water10,863603
1
B: ACTIN, ALPHA SKELETAL MUSCLE
N: PHOSPHATASE AND ACTIN REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,10610
Polymers45,8082
Non-polymers1,2978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-19.7 kcal/mol
Surface area15940 Å2
MethodPISA
2
A: ACTIN, ALPHA SKELETAL MUSCLE
M: PHOSPHATASE AND ACTIN REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7976
Polymers45,8082
Non-polymers9894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-20.4 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.121, 75.924, 122.451
Angle α, β, γ (deg.)90.00, 97.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABMN

#1: Protein ACTIN, ALPHA SKELETAL MUSCLE / ALPHA SKELETAL MUSCLE ACTIN / ALPHA-ACTIN-1


Mass: 41965.754 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-377 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P68135
#2: Protein/peptide PHOSPHATASE AND ACTIN REGULATOR 1 / PHOSPHATASE AND ACTIN REGULATOR 1\ / ISOFORM CRA_C


Mass: 3842.494 Da / Num. of mol.: 2 / Fragment: RESIDUES 138-162 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: G5E8P7, UniProt: Q2M3X8*PLUS

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Non-polymers , 6 types, 615 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 81005 / % possible obs: 96 % / Observed criterion σ(I): 1.4 / Redundancy: 2.6 % / Biso Wilson estimate: 17.16 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 3.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.4 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V52

2v52


Resolution: 1.75→29.278 Å / SU ML: 0.22 / σ(F): 0.84 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 3908 5 %
Rwork0.1795 --
obs0.1816 77602 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5943 0 146 603 6692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076340
X-RAY DIFFRACTIONf_angle_d1.1658621
X-RAY DIFFRACTIONf_dihedral_angle_d13.3412401
X-RAY DIFFRACTIONf_chiral_restr0.077965
X-RAY DIFFRACTIONf_plane_restr0.0061092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81260.33883680.2917076X-RAY DIFFRACTION92
1.8126-1.88510.31423920.26487446X-RAY DIFFRACTION98
1.8851-1.97090.26563940.23117499X-RAY DIFFRACTION98
1.9709-2.07480.23213820.19457490X-RAY DIFFRACTION98
2.0748-2.20470.22084110.17467487X-RAY DIFFRACTION98
2.2047-2.37490.22353930.16817426X-RAY DIFFRACTION97
2.3749-2.61370.22473810.1687423X-RAY DIFFRACTION97
2.6137-2.99160.21844240.16697365X-RAY DIFFRACTION96
2.9916-3.76790.20073700.16297359X-RAY DIFFRACTION95
3.7679-29.28180.1843930.1577123X-RAY DIFFRACTION91
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)
11.3907-0.26620.28321.6535-0.29472.36680.0920.2291-0.0125-0.3666-0.0445-0.03950.05450.029-0.03970.15780.00960.02490.12250.0090.0633-3.3035-3.6615-19.9976
24.9172-1.3941.80822.844-1.43055.99920.190.62580.9117-0.5584-0.13330.6182-0.7661-0.32290.13940.25970.1164-0.02320.30710.08540.3601-18.9219.8513-17.3566
30.802-0.6062-0.65962.43440.14660.9965-0.0575-0.1279-0.08180.25-0.0314-0.1250.10890.0920.06630.09510.006-0.00130.10830.03440.11-5.3116-12.87052.8138
41.9914-0.65160.04472.1684-0.11590.7691-0.0804-0.13380.07880.34970.05390.0625-0.0845-0.10590.01990.14070.01610.04340.13290.00130.0901-21.22235.13188.856
51.65220.3709-0.6461.6837-0.37862.17330.1084-0.280.03260.4353-0.0331-0.1005-0.10760.1071-0.06580.1629-0.0151-0.03240.118600.0854.287421.2694-40.9243
61.53952.1587-1.34734.7993-3.80094.3979-0.0856-0.3641-0.65490.04640.13780.34770.5922-0.2611-0.00360.246-0.0420.02810.21830.07790.3084-12.21826.487-41.8526
70.94680.46120.52882.29330.1031.1738-0.06480.09380.0505-0.23230.0174-0.1369-0.09440.06430.03360.0744-0.01310.01030.09020.02410.12921.655330.2856-63.8251
81.71841.15220.14842.5644-0.32221.2598-0.06510.1066-0.065-0.34150.02530.08030.1171-0.11730.03230.12420.0001-0.04860.1213-0.00620.1443-13.763812.3224-69.6495
92.34551.4161-0.39173.35880.73291.63790.08380.1868-0.26350.1273-0.0807-0.31020.2133-0.1361-0.02120.17670.02150.02170.21140.02920.39386.1174-21.1856-10.5968
102.7672-1.72690.53783.53160.48531.32940.1104-0.01420.15480.0926-0.1335-0.2766-0.1484-0.0898-0.0010.181-0.02690.04870.18880.00930.397113.329338.7423-50.061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5:32 OR RESID 70:144 OR RESID 338:375)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 33:69)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 145:180 OR RESID 270:337)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 181:269)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 5:32 OR RESID 70:144 OR RESID 338:375)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 33:69)
7X-RAY DIFFRACTION7CHAIN B AND (RESID 145:180 OR RESID 270:337)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 181:269)
9X-RAY DIFFRACTION9CHAIN M
10X-RAY DIFFRACTION10CHAIN N

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