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- PDB-4xh3: Mechanistic insights into anchorage of the contractile ring from ... -

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Basic information

Entry
Database: PDB / ID: 4xh3
TitleMechanistic insights into anchorage of the contractile ring from yeast to humans
ComponentsActin-binding protein anillin
KeywordsCELL CYCLE / C2
Function / homology
Function and homology information


positive regulation of bleb assembly / septin ring organization / actomyosin contractile ring assembly / septin ring assembly / podocyte cell migration / actomyosin contractile ring / bleb / regulation of exit from mitosis / RHOB GTPase cycle / RHOC GTPase cycle ...positive regulation of bleb assembly / septin ring organization / actomyosin contractile ring assembly / septin ring assembly / podocyte cell migration / actomyosin contractile ring / bleb / regulation of exit from mitosis / RHOB GTPase cycle / RHOC GTPase cycle / mitotic cytokinesis / RHOA GTPase cycle / hematopoietic progenitor cell differentiation / actin cytoskeleton / actin binding / cell cortex / midbody / cadherin binding / nucleoplasm / cytosol
Similarity search - Function
Anillin homology domain / Anillin, N-terminal domain / Anillin, PH domain / Cell division protein anillin / Anillin N-terminus / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsSun, L.F. / Guan, R.F. / Chen, Z.C.
Funding support China, United States, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270762 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086546 United States
CitationJournal: Dev.Cell / Year: 2015
Title: Mechanistic insights into the anchorage of the contractile ring by anillin and mid1
Authors: Sun, L. / Guan, R. / Lee, I.J. / Liu, Y. / Chen, M. / Wang, J. / Wu, J.Q. / Chen, Z.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-binding protein anillin


Theoretical massNumber of molelcules
Total (without water)46,7651
Polymers46,7651
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.148, 126.116, 54.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Actin-binding protein anillin


Mass: 46765.293 Da / Num. of mol.: 1 / Fragment: UNP residues 675-1087
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANLN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.64 Å3/Da / Density % sol: 25.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) glycerol, 18% PEG 1500, 100 mM Hepes, 5 mM DTT

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→37 Å / Num. obs: 17691 / % possible obs: 96.11 % / Redundancy: 4.8 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 2.1→36.669 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 884 5 %
Rwork0.218 --
obs0.2194 17691 96.11 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.894 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-34.15 Å2-0 Å2-0 Å2
2---4.1228 Å2-0 Å2
3----30.0272 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 63 1717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071679
X-RAY DIFFRACTIONf_angle_d0.932269
X-RAY DIFFRACTIONf_dihedral_angle_d11.896626
X-RAY DIFFRACTIONf_chiral_restr0.062275
X-RAY DIFFRACTIONf_plane_restr0.003288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.23160.40681290.36532463X-RAY DIFFRACTION87
2.2316-2.40390.40911460.34252762X-RAY DIFFRACTION96
2.4039-2.64570.33031510.27922868X-RAY DIFFRACTION99
2.6457-3.02840.30511510.23912881X-RAY DIFFRACTION99
3.0284-3.81490.22741530.1972908X-RAY DIFFRACTION99
3.8149-36.67480.18291540.17842925X-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)
15.2595-3.9767-3.42792.85032.52572.0743-0.46010.482-0.2472-0.48250.46890.10390.64730.30860.02810.71590.0550.01040.7855-0.06550.610342.973718.410550.573
21.2210.758-0.62874.0337-4.06537.36370.0564-0.25090.03420.3826-0.2201-0.0771-0.99070.67490.1660.4036-0.06820.00670.472-0.00760.476536.727735.539536.5537
32.1543-2.7978-2.23882.06993.30972.2210.28840.40590.3522-0.3701-0.2623-0.0658-1.06290.46350.0440.9426-0.07720.06940.45620.08070.738737.64946.114914.5883
41.66970.8007-1.95541.618-1.73565.8695-0.09220.03440.0366-0.27640.0704-0.06590.5047-0.1341-0.00180.3971-0.0696-0.01510.44750.0030.433733.740231.144928.8332
51.6820.88130.33877.6498-6.16438.327-0.76550.3451-0.53830.45230.40340.01161.5802-0.51950.04730.6888-0.00360.07210.5835-0.02720.578328.829219.674948.6374
62.9808-2.23293.00274.0989-4.91227.60680.3210.3664-0.0930.0102-0.4656-0.1690.49650.98030.13960.5686-0.0973-0.05360.56350.07330.516338.773111.599320.636
71.17522.2177-1.59885.6316-2.37553.43680.4661-0.00810.2158-0.1339-0.2260.5152-0.9636-0.3516-0.12070.59090.0580.0410.52340.04260.454729.763728.34230.6415
80.98280.32050.03083.04960.75361.50280.1838-0.08250.00020.3542-0.1669-0.0335-0.02260.15680.07680.3977-0.0752-0.01220.50630.05740.462335.776521.564919.9901
92.40420.3093-0.4493.2671-1.92171.107-0.19660.33180.3712-0.0427-0.05330.0587-0.3583-0.6615-0.00140.73420.0345-0.01040.62160.04120.564128.679240.529420.7243
101.2514-0.05030.45081.634-0.90650.59920.12060.0891-0.19390.1521-0.06280.31440.19380.0347-0.02330.537-0.0629-0.01410.4930.02590.452228.571514.20619.8688
114.0445-2.05141.60582.1551-1.54771.2710.18580.08130.0158-0.3159-0.13960.08890.2133-0.1410.02130.48-0.01810.0510.58360.02210.477225.39419.145612.1559
120.62950.3798-0.10727.0905-8.28622.01040.520.3265-0.2291-0.4385-0.0833-0.72780.48520.79380.24260.76260.0205-0.03810.61580.00240.754140.70364.177524.445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -2:6)
2X-RAY DIFFRACTION2(chain A and resid 7:33)
3X-RAY DIFFRACTION3(chain A and resid 34:44)
4X-RAY DIFFRACTION4(chain A and resid 45:64)
5X-RAY DIFFRACTION5(chain A and resid 65:75)
6X-RAY DIFFRACTION6(chain A and resid 90:101)
7X-RAY DIFFRACTION7(chain A and resid 102:114)
8X-RAY DIFFRACTION8(chain A and resid 115:175)
9X-RAY DIFFRACTION9(chain A and resid 176:226)
10X-RAY DIFFRACTION10(chain A and resid 227:249)
11X-RAY DIFFRACTION11(chain A and resid 250:263)
12X-RAY DIFFRACTION12(chain A and resid 264:269)

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