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- PDB-6jbk: Crystal structure of an actin monomer in complex with the nucleat... -

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Basic information

Entry
Database: PDB / ID: 6jbk
TitleCrystal structure of an actin monomer in complex with the nucleator Cordon-Bleu WH2-motif peptide mutant. T22V
Components
  • Actin, alpha skeletal muscle
  • Peptide from Protein cordon-bleu
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / WH2 / actin / sequestering / PROTEIN BINDING / STRUCTURAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


somite specification / floor plate development / actin filament network formation / terminal web / embryonic axis specification / notochord development / actin crosslink formation / collateral sprouting in absence of injury / digestive tract development / positive regulation of ruffle assembly ...somite specification / floor plate development / actin filament network formation / terminal web / embryonic axis specification / notochord development / actin crosslink formation / collateral sprouting in absence of injury / digestive tract development / positive regulation of ruffle assembly / positive regulation of dendrite development / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / dendritic growth cone / 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 / axonal growth cone / stress fiber / titin binding / ruffle / actin filament polymerization / liver development / filopodium / neural tube closure / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell cortex / cell body / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / axon / neuronal cell body / calcium ion binding / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Protein cordon-bleu
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsScipion, C.P.M. / Robinson, R.C.
CitationJournal: To Be Published
Title: Design of an actin-severing peptide
Authors: Scipion, C.P.M. / Robinson, R.C.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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: Peptide from Protein cordon-bleu
C: Actin, alpha skeletal muscle
D: Peptide from Protein cordon-bleu
E: Actin, alpha skeletal muscle
F: Peptide from Protein cordon-bleu
G: Actin, alpha skeletal muscle
H: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,44020
Polymers178,0918
Non-polymers2,34912
Water8,017445
1
A: Actin, alpha skeletal muscle
B: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1105
Polymers44,5232
Non-polymers5873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-39 kcal/mol
Surface area16120 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1105
Polymers44,5232
Non-polymers5873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-38 kcal/mol
Surface area16170 Å2
MethodPISA
3
E: Actin, alpha skeletal muscle
F: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1105
Polymers44,5232
Non-polymers5873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-38 kcal/mol
Surface area16250 Å2
MethodPISA
4
G: Actin, alpha skeletal muscle
H: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1105
Polymers44,5232
Non-polymers5873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-39 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.220, 81.192, 89.869
Angle α, β, γ (deg.)90.62, 107.19, 109.63
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Escherichia coli (E. coli) / References: UniProt: P68135
#2: Protein/peptide
Peptide from Protein cordon-bleu


Mass: 2412.812 Da / Num. of mol.: 4 / Mutation: T22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cobl, Kiaa0633 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5NBX1
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.13 Å3/Da / Density % sol: 42.38 % / Description: three-dimensional dagger blade like crystals
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20mM MES, pH 4.5, 0.2mM CaCl2.2H2O, 11% PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→85.21 Å / Num. obs: 49603 / % possible obs: 94.5 % / Redundancy: 1.9 % / Net I/σ(I): 17.7
Reflection shellResolution: 2.45→2.493 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YPU

5ypu


Resolution: 2.45→19.965 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.34
RfactorNum. reflection% reflection
Rfree0.2389 2473 5 %
Rwork0.1867 --
obs0.1893 49490 91.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11701 0 132 445 12278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512073
X-RAY DIFFRACTIONf_angle_d1.00216382
X-RAY DIFFRACTIONf_dihedral_angle_d13.2297261
X-RAY DIFFRACTIONf_chiral_restr0.0571836
X-RAY DIFFRACTIONf_plane_restr0.0083565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4461-2.4930.2899840.23281740X-RAY DIFFRACTION61
2.493-2.54380.28871040.23572199X-RAY DIFFRACTION75
2.5438-2.5990.26931020.23682299X-RAY DIFFRACTION81
2.599-2.65940.34141070.2262561X-RAY DIFFRACTION88
2.6594-2.72570.26481450.21312656X-RAY DIFFRACTION94
2.7257-2.79920.25191610.2112779X-RAY DIFFRACTION96
2.7992-2.88130.27391470.21642747X-RAY DIFFRACTION97
2.8813-2.9740.29651490.22842719X-RAY DIFFRACTION96
2.974-3.080.27981410.21412774X-RAY DIFFRACTION96
3.08-3.20280.26071500.20372749X-RAY DIFFRACTION96
3.2028-3.34790.26871510.20712730X-RAY DIFFRACTION97
3.3479-3.52350.24411470.18722769X-RAY DIFFRACTION96
3.5235-3.74290.21021480.17532760X-RAY DIFFRACTION96
3.7429-4.02980.19961440.16482717X-RAY DIFFRACTION96
4.0298-4.43130.2291750.15492741X-RAY DIFFRACTION96
4.4313-5.06330.21561200.14242721X-RAY DIFFRACTION94
5.0633-6.34510.20791380.1842628X-RAY DIFFRACTION91
6.3451-19.96530.20211600.16322728X-RAY DIFFRACTION96
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)
11.239-0.40330.12212.0638-0.34131.2559-0.0309-0.0646-0.04690.11190.0777-0.11280.04020.188-0.05520.2246-0.0152-0.03870.2209-0.0290.203410.616716.992420.3272
21.4325-0.7068-0.44761.2840.59251.755-0.0463-0.3080.28040.16280.2016-0.0489-0.10060.2974-0.16590.2754-0.05470.03160.266-0.03040.31220.973533.362927.5056
30.9721-0.34860.35230.92440.11870.94120.0047-0.05120.05890.0011-0.0660.14360.0152-0.22310.05390.1923-0.02320.01550.2502-0.00180.307-6.701626.837420.3752
45.1438-2.50260.79246.11363.89743.86170.60250.0245-0.2468-0.64930.0315-0.19230.14640.0585-0.42830.6399-0.0914-0.16160.362-0.06930.5068-7.11475.59416.8728
50.38390.20090.23652.15190.30832.22630.14980.01560.09620.21720.09210.11220.1066-0.08810.1010.3966-0.3079-0.0990.21870.1170.717-5.80154.34425.182
61.5538-0.1081-0.32032.0428-0.43831.26960.0105-0.0278-0.01660.151-0.1524-0.2709-0.15990.32420.1140.1901-0.0435-0.00620.28490.03890.2862-2.3541-21.485521.2477
70.6174-0.37250.12160.62540.78921.8123-0.00870.04440.24820.10580.0521-0.0296-0.12530.1235-0.07510.2872-0.05250.01020.19770.00610.3156-16.2632-7.188223.9201
80.2162-0.14440.15190.53250.36591.0115-0.00360.03230.04120.0109-0.09490.0677-0.1409-0.23460.08380.19660.02220.0090.26690.00070.271-26.2273-7.689522.8727
93.83131.3566-2.15850.5703-0.65761.31840.0650.5121-0.521-0.1121-0.1359-0.3305-0.0664-0.0430.01390.35650.03670.09060.3729-0.00170.3965-2.9419-31.94136.1118
104.6436-1.0767-0.21194.87691.71677.71530.4640.0743-0.8524-0.59110.2304-0.27870.4095-0.0012-0.48820.4671-0.01980.04210.322-0.04670.3813-21.8144-33.32846.8133
113.3050.23650.68373.2320.67691.41760.00450.01010.00050.3685-0.3428-0.1160.07220.36180.24680.417-0.19060.08470.32050.01280.5652-20.3975-34.221824.8349
122.12330.1757-0.50250.529-0.20520.98330.00740.12230.071-0.0514-0.01210.0146-0.1018-0.0347-0.00670.26750.02750.02870.1905-0.00690.1735-3.8506-18.1281-24.7165
131.6325-0.12390.07070.3108-0.12971.30580.0435-0.1154-0.1171-0.0665-0.1047-0.03430.09110.28850.06790.20350.02590.04110.18870.00790.21416.4913-24.4734-20.6056
143.7910.48960.30772.8221-1.41114.84140.9211-0.9819-0.49380.15850.36860.0703-0.0213-0.2189-0.78920.5608-0.0689-0.04710.3960.15050.7326-6.387-38.9497-7.2948
150.7896-0.77271.05921.2096-1.47962.2447-0.11220.1525-0.1358-0.3859-0.3697-0.01680.2654-0.46770.45240.66220.0287-0.10740.2521-0.04220.6452-7.5787-40.3296-25.4476
162.0218-0.25250.16691.09150.38331.7499-0.04790.11320.1095-0.3644-0.01390.0759-0.5566-0.1283-0.01220.50850.0462-0.05930.2432-0.00520.22672.488821.0245-22.9397
170.8079-0.0494-0.6497-0.1578-0.52592.90040.0353-0.05180.06970.0424-0.1003-0.0169-0.25930.4740.07370.3143-0.0435-0.04580.27440.00560.241926.43815.5652-25.3927
181.6047-1.2861-0.42723.47860.95672.05030.0118-0.5757-0.20610.28630.15070.3252-0.172-0.4731-0.13370.3483-0.0286-0.00830.42420.01640.3815-4.601913.6904-7.637
194.631.5602-0.42632.0391-2.76656.38391.1415-1.1119-0.22340.61610.11751.13030.0005-0.2339-0.7840.6033-0.14930.07780.49310.08690.57337.4276-0.2843-7.6607
201.34590.2362-0.08342.0636-1.01242.4951-0.0664-0.07130.00380.1001-0.23790.1057-0.4681-0.19320.29850.4745-0.01090.02130.2631-0.03120.29116.2134-1.2454-25.6815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 165 )
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 372 )
4X-RAY DIFFRACTION4chain 'B' and (resid 66 through 78 )
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 87 )
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 145 )
7X-RAY DIFFRACTION7chain 'C' and (resid 146 through 216 )
8X-RAY DIFFRACTION8chain 'C' and (resid 217 through 348 )
9X-RAY DIFFRACTION9chain 'C' and (resid 349 through 372 )
10X-RAY DIFFRACTION10chain 'D' and (resid 66 through 77 )
11X-RAY DIFFRACTION11chain 'D' and (resid 78 through 87 )
12X-RAY DIFFRACTION12chain 'E' and (resid 5 through 232 )
13X-RAY DIFFRACTION13chain 'E' and (resid 233 through 372 )
14X-RAY DIFFRACTION14chain 'F' and (resid 66 through 76 )
15X-RAY DIFFRACTION15chain 'F' and (resid 77 through 87 )
16X-RAY DIFFRACTION16chain 'G' and (resid 5 through 145 )
17X-RAY DIFFRACTION17chain 'G' and (resid 146 through 348 )
18X-RAY DIFFRACTION18chain 'G' and (resid 349 through 372 )
19X-RAY DIFFRACTION19chain 'H' and (resid 66 through 76 )
20X-RAY DIFFRACTION20chain 'H' and (resid 77 through 87 )

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