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- PDB-4b1x: Structure of the Phactr1 RPEL-2 bound to G-actin -

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Basic information

Entry
Database: PDB / ID: 4b1x
TitleStructure of the Phactr1 RPEL-2 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: 1.8 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 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
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 1.3Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Jun 20, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value
Revision 1.5Dec 20, 2023Group: 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
B: ACTIN, ALPHA SKELETAL MUSCLE
M: PHOSPHATASE AND ACTIN REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7615
Polymers45,8342
Non-polymers9273
Water3,801211
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29.3 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.280, 77.280, 130.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BM

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


Mass: 41965.754 Da / Num. of mol.: 1 / 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: 3868.409 Da / Num. of mol.: 1 / Fragment: RESIDUES 524-555 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: G5E8P7, UniProt: Q2M3X8*PLUS

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Non-polymers , 4 types, 214 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: ID23-1 / Type: DIAMOND / Wavelength: 0.9763
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 69989 / % possible obs: 98.7 % / Observed criterion σ(I): 1.1 / Redundancy: 5.6 % / Biso Wilson estimate: 26.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

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Processing

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

2v52


Resolution: 1.8→38.64 Å / SU ML: 0.19 / σ(F): 1.42 / Phase error: 21.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2127 2058 5.1 %
Rwork0.1688 --
obs0.171 40540 95.19 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 59 211 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073185
X-RAY DIFFRACTIONf_angle_d1.1284346
X-RAY DIFFRACTIONf_dihedral_angle_d19.8871260
X-RAY DIFFRACTIONf_chiral_restr0.077493
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84190.32281160.2352335X-RAY DIFFRACTION88
1.8419-1.88790.28731420.23342384X-RAY DIFFRACTION90
1.8879-1.9390.27141330.20812409X-RAY DIFFRACTION92
1.939-1.9960.24471480.19612523X-RAY DIFFRACTION95
1.996-2.06050.25461490.19172556X-RAY DIFFRACTION96
2.0605-2.13410.2571420.18912543X-RAY DIFFRACTION96
2.1341-2.21950.24941270.18012604X-RAY DIFFRACTION97
2.2195-2.32050.23711100.18352631X-RAY DIFFRACTION98
2.3205-2.44290.20811320.17012639X-RAY DIFFRACTION98
2.4429-2.59590.24531480.17842584X-RAY DIFFRACTION97
2.5959-2.79630.23981420.17252643X-RAY DIFFRACTION97
2.7963-3.07760.2261530.17592615X-RAY DIFFRACTION97
3.0776-3.52260.18981510.16892656X-RAY DIFFRACTION97
3.5226-4.43710.18091280.13922626X-RAY DIFFRACTION96
4.4371-38.64890.16891370.15282734X-RAY DIFFRACTION94
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)
14.01830.32140.36616.3832-1.96885.4981-0.0096-0.2098-0.45220.0210.1613-0.58220.20280.295-0.15270.13950.02440.00240.2176-0.08370.28476.8176-43.902211.1065
24.5016-0.3895-3.44180.2092-0.02184.22110.49760.64770.5962-0.8218-0.1392-1.0099-0.34221.1673-0.34540.5070.01330.25660.4913-0.10840.456113.6855-34.9659-1.6975
32.7187-0.6217-0.60772.34780.40492.10090.11550.3418-0.2231-0.6239-0.0837-0.2545-0.1695-0.0017-0.02850.29050.01020.04590.2535-0.09860.2224.2873-40.9331.7019
44.23071.4403-1.10272.4553-0.35581.23980.01720.20140.385-0.33820.1265-0.1261-0.1773-0.0408-0.09410.20070.00690.04640.1751-0.05890.2318-0.0992-23.557210.4615
52.1686-0.1347-0.60691.19120.56251.15060.4488-0.02481.286-0.22040.04910.2481-0.47720.2326-0.0250.3486-0.07020.21050.2106-0.22620.56535.3359-11.08416.9436
65.8020.3785-0.51912.1862-0.00010.14920.0823-0.48610.15470.13980.03160.1911-0.0837-0.0246-0.11820.1554-0.00530.03920.2736-0.08110.1696-12.3639-27.514821.1628
72.0114-1.2772-0.48642.73331.01940.8470.0374-0.53610.1810.4026-0.10530.22450.0826-0.04730.0020.1596-0.00480.04610.3386-0.13230.2316-4.3272-30.307723.6135
84.61940.59243.18342.84192.9135.437-0.1204-0.1049-1.07850.3608-0.39770.69720.7965-0.70280.04970.3446-0.10660.03850.3145-0.16920.6451-8.7735-54.50846.9793
94.8786-0.4401-0.05613.93190.61512.2867-0.2156-0.4468-0.89430.1376-0.38470.41620.5796-0.09340.35280.218-0.00320.08160.35520.03410.3497-17.705-45.089219.3266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 0:28)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 29:61)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 62:145)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 146:216)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 217:273)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 274:308)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 309:348)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 349:375)
9X-RAY DIFFRACTION9CHAIN M

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