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- PDB-4jhd: Crystal Structure of an Actin Dimer in Complex with the Actin Nuc... -

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Basic information

Entry
Database: PDB / ID: 4jhd
TitleCrystal Structure of an Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu
Components
  • (Actin-5C) x 2
  • Protein cordon-bleu
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / actin cytoskeleton / actin filament nucleator / nuclear actin / nucleation / tandem W domains / STRUCTURAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


somite specification / Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway / ovarian fusome organization ...somite specification / Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway / ovarian fusome organization / floor plate development / Platelet degranulation / MAP2K and MAPK activation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / DNA Damage Recognition in GG-NER / Clathrin-mediated endocytosis / actin filament network formation / UCH proteinases / sperm individualization / terminal web / embryonic axis specification / notochord development / actin crosslink formation / maintenance of protein location in cell / brahma complex / tube formation / digestive tract development / Ino80 complex / collateral sprouting in absence of injury / positive regulation of ruffle assembly / positive regulation of dendrite development / dendritic growth cone / mitotic cytokinesis / actin monomer binding / axonal growth cone / ruffle / actin filament polymerization / liver development / neural tube closure / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell cortex / actin cytoskeleton organization / cytoskeleton / hydrolase activity / chromatin remodeling / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / ATP 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. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...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. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Actin-5C / Protein cordon-bleu
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsChen, X. / Ni, F. / Wang, Q.
CitationJournal: Cell Rep / Year: 2013
Title: Structural basis of actin filament nucleation by tandem w domains.
Authors: Chen, X. / Ni, F. / Tian, X. / Kondrashkina, E. / Wang, Q. / Ma, J.
History
DepositionMar 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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.value / _struct_conn.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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-5C
B: Actin-5C
C: Protein cordon-bleu
D: Actin-5C
E: Actin-5C
F: Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,23514
Polymers208,1136
Non-polymers2,1228
Water2,846158
1
A: Actin-5C
B: Actin-5C
C: Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1187
Polymers104,0573
Non-polymers1,0614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-69 kcal/mol
Surface area34300 Å2
MethodPISA
2
D: Actin-5C
E: Actin-5C
F: Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1187
Polymers104,0573
Non-polymers1,0614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-71 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.450, 99.800, 118.270
Angle α, β, γ (deg.)65.41, 90.03, 77.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41E
12A
22B
32D
42E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAHISHISAA6 - 4015 - 49
21ALAALAHISHISBB6 - 4015 - 49
31ALAALAHISHISDD6 - 4015 - 49
41ALAALAHISHISEE6 - 4015 - 49
12TYRTYRHISHISAA53 - 37162 - 380
22TYRTYRHISHISBB53 - 37162 - 380
32TYRTYRHISHISDD53 - 37162 - 380
42TYRTYRHISHISEE53 - 37162 - 380
13HISHISLEULEUCC68 - 13520 - 87
23HISHISLEULEUFF68 - 13520 - 87

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Actin-5C


Mass: 42989.012 Da / Num. of mol.: 2 / Mutation: A204E, P243K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10987
#2: Protein Actin-5C


Mass: 42930.914 Da / Num. of mol.: 2 / Mutation: K291E, P322K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10987
#3: Protein Protein cordon-bleu


Mass: 18136.596 Da / Num. of mol.: 2 / Fragment: WH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cobl, Kiaa0633 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NBX1

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Non-polymers , 3 types, 166 molecules

#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO UNIPROT SEQUENCE DATABASE THERE ARE SEQUENCE CONFLICTS AT THESE TWO POSITIONS.

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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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 10% PEG3350, 0.18M NaCl, 0.1M PIPES, protein:mother liquor = 2:1, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.91→45.021 Å / Num. all: 47394 / Num. obs: 46301 / % possible obs: 97.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.91-2.9705196
2.9705-3.0351199
3.0351-3.1057197
3.1057-3.1833197
3.1833-3.2693198
3.2693-3.3655197
3.3655-3.4741198
3.4741-3.5982197
3.5982-3.7422198
3.7422-3.9124198
3.9124-4.1186197
4.1186-4.3764199
4.3764-4.714198
4.714-5.1878198
5.1878-5.937197
5.937-7.4744199
7.4744-45.0261198

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→45.02 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.349 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 0.968 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25512 2341 5.1 %RANDOM
Rwork0.20042 ---
obs0.20317 43972 97.71 %-
all-47394 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.709 Å2
Baniso -1Baniso -2Baniso -3
1--3.28 Å21.11 Å2-1.81 Å2
2---0.33 Å2-1.03 Å2
3---3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.91→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12716 0 128 158 13002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.97917758
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47151634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4623.804552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.503152271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3911586
X-RAY DIFFRACTIONr_chiral_restr0.0760.21975
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029764
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.26149
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.28955
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2515
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.2163
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2470.54
12B2470.53
13D2470.67
14E2470.58
21A24880.41
22B24880.37
23D24880.56
24E24880.37
31C5100.87
LS refinement shellResolution: 2.91→2.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 168 -
Rwork0.284 3236 -
obs--96.46 %

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