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- PDB-4d1e: THE CRYSTAL STRUCTURE OF HUMAN MUSCLE ALPHA-ACTININ-2 -

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Basic information

Entry
Database: PDB / ID: 4d1e
TitleTHE CRYSTAL STRUCTURE OF HUMAN MUSCLE ALPHA-ACTININ-2
ComponentsALPHA-ACTININ-2
KeywordsCONTRACTILE PROTEIN / Z-DISC / CALMODULIN-LIKE DOMAIN / SPECTRIN DOMAIN / ACTIN BINDING DOMAIN / ABD
Function / homology
Function and homology information


actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / positive regulation of cation channel activity / LIM domain binding ...actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / positive regulation of cation channel activity / LIM domain binding / microspike assembly / postsynaptic actin cytoskeleton / positive regulation of potassium ion transport / muscle cell development / focal adhesion assembly / Striated Muscle Contraction / Assembly and cell surface presentation of NMDA receptors / Nephrin family interactions / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / negative regulation of potassium ion transport / Long-term potentiation / postsynaptic density, intracellular component / phosphatidylinositol-4,5-bisphosphate binding / titin binding / cytoskeletal protein binding / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / platelet alpha granule lumen / nuclear receptor coactivator activity / filopodium / cell projection / protein localization to plasma membrane / actin filament / postsynaptic density membrane / Z disc / actin filament binding / integrin binding / cell junction / Platelet degranulation / actin cytoskeleton organization / RAF/MAP kinase cascade / regulation of apoptotic process / transmembrane transporter binding / dendritic spine / cytoskeleton / cell adhesion / protein domain specific binding / focal adhesion / glutamatergic synapse / calcium ion binding / extracellular exosome / extracellular region / identical protein binding / cytosol
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPinotsis, N. / Salmazo, A. / Sjoeblom, B. / Gkougkoulia, E. / Djinovic-Carugo, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: The Structure and Regulation of Human Muscle Alpha-Actinin
Authors: Ribeiro Jr, E.A. / Pinotsis, N. / Ghisleni, A. / Salmazo, A. / Konarev, P.V. / Kostan, J. / Sjoeblom, B. / Schreiner, C. / Polyansky, A.A. / Gkougkoulia, E. / Holt, M.R. / Aachmann, F.L. / ...Authors: Ribeiro Jr, E.A. / Pinotsis, N. / Ghisleni, A. / Salmazo, A. / Konarev, P.V. / Kostan, J. / Sjoeblom, B. / Schreiner, C. / Polyansky, A.A. / Gkougkoulia, E. / Holt, M.R. / Aachmann, F.L. / Zagrovic, B. / Bordignon, E. / Pirker, K.F. / Svergun, D.I. / Gautel, M. / Djinovic-Carugo, K.
History
DepositionMay 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 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_conn
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_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: ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)101,8551
Polymers101,8551
Non-polymers00
Water00
1
A: ALPHA-ACTININ-2

A: ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)203,7092
Polymers203,7092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_574x,-y+2,-z-11
Buried area9000 Å2
ΔGint-48.7 kcal/mol
Surface area94480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.334, 102.613, 182.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein ALPHA-ACTININ-2 / ALPHA-ACTININ SKELETAL MUSCLE ISOFORM 2 / F-ACTIN CROSS-LINKING PROTEIN


Mass: 101854.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-894 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELTA 1-18 LYSINE METHYLATION / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P35609

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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: 3.48 Å3/Da / Density % sol: 64.65 % / Description: NONE
Crystal growDetails: 0.2 M MG FORMATE 5% PEG SMEAR, 0.01 M EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→51.31 Å / Num. obs: 18047 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Biso Wilson estimate: 97.7 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.2
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1WKU, 1HCI ,1H8B

1wku

1hci

1h8b


Resolution: 3.5→51.307 Å / SU ML: 0.36 / σ(F): 1.91 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 920 5.1 %
Rwork0.2047 --
obs0.2074 18003 99.75 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→51.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6865 0 0 0 6865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116996
X-RAY DIFFRACTIONf_angle_d1.5929451
X-RAY DIFFRACTIONf_dihedral_angle_d22.1252654
X-RAY DIFFRACTIONf_chiral_restr0.1181039
X-RAY DIFFRACTIONf_plane_restr0.0071241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.68450.38161280.28272376X-RAY DIFFRACTION100
3.6845-3.91530.32561470.25422372X-RAY DIFFRACTION100
3.9153-4.21750.29941300.21292403X-RAY DIFFRACTION100
4.2175-4.64170.20481320.17882426X-RAY DIFFRACTION100
4.6417-5.31270.23891360.16852413X-RAY DIFFRACTION99
5.3127-6.69110.27171260.25432484X-RAY DIFFRACTION100
6.6911-51.3120.22421210.17912609X-RAY DIFFRACTION100
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)
17.46022.48250.88192.71721.22880.90510.0727-0.76960.82050.316-0.19240.35050.1699-0.09380.10210.5691-0.09570.01720.6611-0.03470.6743-23.8573236.3021-171.5292
20.9446-0.67010.21634.3857-1.34981.6445-0.14970.4711-0.009-0.29660.26120.4851-0.2814-0.0512-0.01981.57020.15180.16281.43540.57761.2081-14.3838178.7968-140.3602
31.8646-0.4451-0.56836.1976-2.31971.28830.2570.40380.6-2.2673-0.2843-0.49650.20430.0146-0.00471.49770.10490.29070.8190.24870.7659-10.1454126.2053-112.8261
40.4436-0.05280.00769.2858-2.32391.9878-0.0595-0.25640.09590.0328-0.1034-0.6299-0.0931-0.06430.140.38870.016-0.05670.5122-0.03960.5122-12.284670.0292-90.281
53.57810.5756-0.26034.9937-3.27846.3306-0.0597-1.0885-1.3145-0.14910.135-0.12841.3134-0.8199-0.15581.0232-0.1416-0.09430.86510.29130.9727-24.006216.806-58.0747
61.9902-0.6871-1.17853.95220.26393.5691.0402-0.692-0.3698-0.4871-0.4318-0.5469-0.0462-1.0917-0.36191.7591-0.24680.09952.55680.36141.9307-38.87213.4737-33.9135
70.2669-0.0428-0.43822.4714-0.62480.993-0.5565-0.8109-0.2311.39930.4671-0.3198-1.10930.03970.12812.2425-0.0646-0.34761.49650.41171.5554-8.9889-7.1325-12.3103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 34:282))
2X-RAY DIFFRACTION2CHAIN A AND ((RESSEQ 283:396))
3X-RAY DIFFRACTION3CHAIN A AND ((RESSEQ 397:509))
4X-RAY DIFFRACTION4CHAIN A AND ((RESSEQ 510:634))
5X-RAY DIFFRACTION5CHAIN A AND ((RESSEQ 635:747))
6X-RAY DIFFRACTION6CHAIN A AND ((RESSEQ 748:827))
7X-RAY DIFFRACTION7CHAIN A AND ((RESSEQ 828:892))

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