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- PDB-4jd2: Crystal structure of Bos taurus Arp2/3 complex binding with Mus m... -

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Basic information

Entry
Database: PDB / ID: 4jd2
TitleCrystal structure of Bos taurus Arp2/3 complex binding with Mus musculus GMF
Components
  • (Actin-related protein ...) x 7
  • Glia maturation factor gamma
KeywordsSTRUCTURAL PROTEIN / actin filament polymerization and branching
Function / homology
Function and homology information


actin filament debranching / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis ...actin filament debranching / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / cortical actin cytoskeleton / cilium assembly / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / Neutrophil degranulation / cell projection / growth factor activity / structural constituent of cytoskeleton / actin filament binding / cell migration / site of double-strand break / actin binding / cell cortex / neuron projection / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glia maturation factor / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 21 kDa subunit ARPC3 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 ...Glia maturation factor / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 21 kDa subunit ARPC3 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / Yope Regulator; Chain: A, / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / YVTN repeat-like/Quinoprotein amine dehydrogenase / ATPase, nucleotide binding domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin-related protein 2 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B / Glia maturation factor gamma
Similarity search - Component
Biological speciesBos taurus (cattle)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsNolen, B.J. / Luan, Q.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for regulation of Arp2/3 complex by GMF.
Authors: Luan, Q. / Nolen, B.J.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Sep 18, 2013Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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-related protein 3
B: Actin-related protein 2
C: Actin-related protein 2/3 complex subunit 1B
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5
H: Glia maturation factor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,45514
Polymers240,9728
Non-polymers1,4836
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26730 Å2
ΔGint-123 kcal/mol
Surface area79480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.538, 231.538, 109.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Actin-related protein ... , 7 types, 7 molecules ABCDEFG

#1: Protein Actin-related protein 3 / Actin-2 / Actin-like protein 3


Mass: 47428.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61157
#2: Protein Actin-related protein 2 / Actin-like protein 2


Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A7MB62
#3: Protein Actin-related protein 2/3 complex subunit 1B / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41030.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q58CQ2
#4: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHR7
#5: Protein Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T035
#6: Protein Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa subunit / p20-ARC


Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q148J6
#7: Protein Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


Mass: 16251.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYX9

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Protein , 1 types, 1 molecules H

#8: Protein Glia maturation factor gamma / GMF-gamma


Mass: 16771.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9ERL7

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Non-polymers , 3 types, 6 molecules

#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: 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
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM

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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: 3.52 Å3/Da / Density % sol: 65.1 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.08→35.82 Å / Num. obs: 61305

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→35.82 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 43.455 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 3097 5.1 %RANDOM
Rwork0.2092 ---
obs0.21125 57721 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.03 Å20 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 3.08→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15926 0 90 0 16016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01916360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215653
X-RAY DIFFRACTIONr_angle_refined_deg1.111.96322139
X-RAY DIFFRACTIONr_angle_other_deg0.726336021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85851996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04523.829747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.114152814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1415109
X-RAY DIFFRACTIONr_chiral_restr0.0610.22447
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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
LS refinement shellResolution: 3.08→3.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 213 -
Rwork0.319 3844 -
obs--89.03 %
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)
11.86410.039-0.38940.9664-0.03020.8889-0.0050.04350.3469-0.0383-0.04510.39070.106-0.13180.05010.144-0.12150.05690.1355-0.05820.276938.5643-93.288812.1318
22.3803-0.0561-0.1522.1224-0.55350.8479-0.07140.40060.4292-0.13130.110.5186-0.1842-0.0761-0.03860.3639-0.1937-0.12110.29840.11810.236766.1999-60.6301-11.6883
32.38380.2817-0.02082.8577-0.38041.45580.1994-0.28530.1480.3053-0.2098-0.2146-0.2490.2480.01040.3917-0.2663-0.03310.44420.05320.038497.1346-63.146514.2384
41.72131.63670.26973.58510.33180.60170.1010.0756-0.31070.0862-0.10430.04990.36610.02450.00320.3785-0.1140.07860.2208-0.05570.182850.5769-126.54266.292
52.61020.4184-0.85481.4040.21472.68260.2375-0.57851.30510.4031-0.10320.0964-0.5973-0.1321-0.13430.5171-0.17640.35080.4758-0.65061.232217.0414-68.50238.9969
61.73471.7343-0.29192.8337-0.81050.81030.0529-0.202-0.30090.1122-0.2467-0.28340.07190.15410.19380.2626-0.0740.04390.27040.08760.103582.0359-98.147812.227
72.2356-0.39820.30372.1631-0.48571.3205-0.2138-0.1-0.50280.0923-0.0782-0.6020.25090.37130.2920.2895-0.02310.07570.38340.16670.3905107.0983-97.24017.9711
84.8148-0.7425-0.73174.5954-0.79384.30710.16990.78510.5156-0.3143-0.7574-0.388-0.53260.74950.58750.8249-0.5592-0.11170.89040.43680.319293.4405-44.6811-24.8176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 416
2X-RAY DIFFRACTION2B4 - 388
3X-RAY DIFFRACTION3C1 - 372
4X-RAY DIFFRACTION4D1 - 283
5X-RAY DIFFRACTION5E2 - 174
6X-RAY DIFFRACTION6F3 - 168
7X-RAY DIFFRACTION7G9 - 151
8X-RAY DIFFRACTION8H3 - 140

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