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

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Basic information

Entry
Database: PDB / ID: 4xoh
TitleMechanistic insights into anchorage of the contractile ring from yeast to humans
ComponentsDivision mal foutue 1 protein
KeywordsCELL CYCLE / Mid1
Function / homology
Function and homology information


polo box domain specific binding / mitotic cytokinesis, division site positioning / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / medial cortical node / mitotic actomyosin contractile ring, proximal layer / septin ring organization / mitotic actomyosin contractile ring / medial cortex ...polo box domain specific binding / mitotic cytokinesis, division site positioning / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / medial cortical node / mitotic actomyosin contractile ring, proximal layer / septin ring organization / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / actomyosin contractile ring assembly / cytoskeletal protein-membrane anchor activity / actomyosin contractile ring / mitotic cytokinesis / protein-membrane adaptor activity / phosphatidylinositol-4,5-bisphosphate binding / molecular condensate scaffold activity / nuclear envelope / lipid binding / nucleus
Similarity search - Function
PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Anillin-related medial ring protein mid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.801 Å
AuthorsChen, Z. / Wu, J.-Q. / Wang, J. / Guan, R. / Sun, L. / Lee, I.-J. / Liu, Y. / Chen, M.
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 16, 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_assembly_prop / 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_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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

Downloads & links

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Assembly

Deposited unit
C: Division mal foutue 1 protein
A: Division mal foutue 1 protein
B: Division mal foutue 1 protein


Theoretical massNumber of molelcules
Total (without water)108,5473
Polymers108,5473
Non-polymers00
Water00
1
C: Division mal foutue 1 protein

C: Division mal foutue 1 protein


Theoretical massNumber of molelcules
Total (without water)72,3652
Polymers72,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2170 Å2
ΔGint-10 kcal/mol
Surface area28470 Å2
MethodPISA
2
A: Division mal foutue 1 protein
B: Division mal foutue 1 protein


Theoretical massNumber of molelcules
Total (without water)72,3652
Polymers72,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-6 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.941, 80.941, 314.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Division mal foutue 1 protein


Mass: 36182.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Residues 579-680 and 710-920 from Division mal foutue 1 protein (MID1_SCHPO), linked by GGSTGSSGG
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mid1, dmf1, SPCC4B3.15 / Production host: Escherichia coli (E. coli) / References: UniProt: P78953

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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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% PEG 10000, 100mM MES, 1M LiCl, 2mM DTT, pH 6.0

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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: Feb 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→68.4 Å / Num. obs: 26437 / % possible obs: 86.66 % / Redundancy: 7.9 % / Net I/σ(I): 3.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 2.801→68.4 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1317 4.98 %
Rwork0.2349 --
obs0.2366 26437 86.66 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.925 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.591 Å2-0 Å2-0 Å2
2--15.591 Å2-0 Å2
3----31.1821 Å2
Refinement stepCycle: LAST / Resolution: 2.801→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 0 0 6475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036620
X-RAY DIFFRACTIONf_angle_d0.6698961
X-RAY DIFFRACTIONf_dihedral_angle_d12.9322446
X-RAY DIFFRACTIONf_chiral_restr0.0451018
X-RAY DIFFRACTIONf_plane_restr0.0031141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8007-2.91280.3666520.3471984X-RAY DIFFRACTION31
2.9128-3.04540.3492880.29931696X-RAY DIFFRACTION54
3.0454-3.20590.33741570.29393026X-RAY DIFFRACTION96
3.2059-3.40680.31481660.27863162X-RAY DIFFRACTION100
3.4068-3.66980.28851710.25993201X-RAY DIFFRACTION100
3.6698-4.03910.29661660.25593190X-RAY DIFFRACTION100
4.0391-4.62340.27281650.20123205X-RAY DIFFRACTION100
4.6234-5.82450.23481760.21013273X-RAY DIFFRACTION100
5.8245-68.43790.24271760.22513383X-RAY DIFFRACTION98
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)
12.01933.0598-5.16990.7853-0.93024.5675-0.12690.68560.0270.3901-0.57860.5916-0.0151-0.46980.29070.78610.41920.16562.2461-0.29021.1254-26.56948.5889-27.437
21.98933.12610.98485.4728-0.67565.5976-0.076-0.3448-0.37050.1162-0.1205-0.9558-0.52020.57190.16710.82910.2631-0.09661.33160.01670.8144-1.80789.4715-21.0725
33.59234.2942-1.99927.29321.10585.52130.4062-0.33540.5590.5317-0.50690.1310.17430.09550.08810.70850.4158-0.01741.398-0.09360.7066-9.267810.0927-23.6209
46.09494.45323.18045.2392.14315.0302-0.00960.0840.8090.71570.10730.2698-0.4014-0.61340.01860.72190.4523-0.03281.2912-0.01560.8936-10.457812.6956-29.1569
54.35132.1075-0.49622.01427.25199.8989-0.54450.6021-3.95441.57430.115-1.26541.88680.20720.16080.60550.37830.17151.72460.22191.2347-16.5419-4.8415-34.0201
63.6794-1.69693.51795.7707-3.1345.025-0.3163-0.73231.3873-0.86640.0347-0.5064-1.14271.41210.43770.5805-0.4628-0.21342.134-0.00370.9687-37.670915.3419-53.186
75.9885-2.3356-0.03226.4685-3.23116.5415-0.471-0.21080.48780.62440.3598-0.2891-0.92020.71320.00640.5664-0.1755-0.07261.4977-0.06140.8311-42.042215.8924-51.1943
85.5305-2.2418-0.88546.2083-0.270210.003-0.2053-0.7669-0.3211-0.1769-0.33320.2023-0.1509-0.64540.60370.5022-0.2943-0.04481.4344-0.10810.9161-42.38899.6128-52.7015
96.44941.93740.89674.51191.7547.7598-0.31840.4166-0.83220.2456-0.0797-0.12730.85531.93440.25970.8590.334-0.00232.0605-0.42671.0888-25.2156-6.9945-45.0585
100.2893-0.6303-0.96754.41494.65298.2927-0.1093-0.1825-0.59941.2067-0.1261.64061.4736-1.07330.33190.4644-0.34560.08952.2736-0.31871.1127-27.5611-4.7278-36.6679
114.1841-4.04181.13318.1435-1.19786.1193-1.1008-0.59790.52911.15560.708-0.48390.22370.47330.35710.74170.247-0.04441.2399-0.0620.5334-9.1519-2.1745-12.2754
129.883-5.11212.03268.1666-7.37092.0237-0.3644-1.7862.00950.1372-0.1171-2.464-0.3680.14140.80130.78220.3376-0.12611.497-0.06331.22810.2826-1.4971-15.2997
138.9109-3.7415-2.43248.54462.24458.2456-0.1919-0.0762-0.3754-0.1430.0096-0.04330.4179-0.17670.22930.81980.2705-0.07811.1908-0.03970.4352-7.8371-5.8917-13.3488
143.5226-2.8835-1.48238.69010.61624.202-0.397-0.8001-0.21730.33340.56810.623-0.4307-0.4807-0.16830.74550.4276-0.01651.548-0.01970.6514-15.7568-1.1826-4.0946
159.38362.247-4.55374.8435.23852.0375-1.0317-1.48721.4580.17920.6708-0.099-0.44470.99880.11.20180.6735-0.27921.2687-0.13631.0285-13.613514.96921.9293
161.2036-1.1349-1.95148.71881.49929.3643-0.51760.8056-1.11730.5803-0.03641.3111.91240.60660.52261.20040.3596-0.08621.6162-0.41480.9659-38.137814.97432.4601
174.8752-1.35180.80469.387-1.00245.5170.82871.5879-0.4788-0.7008-1.07111.6770.7123-0.94630.30891.05890.432-0.22061.6495-0.49911.2539-38.31913.483625.5601
183.8837-2.0301-2.68077.14351.7012.1762-0.070.8030.3748-0.3528-1.32661.88160.1327-1.40351.37671.30460.7291-0.14091.8786-0.47851.4394-42.91722.16527.5809
193.44491.21090.13863.28561.56722.01891.26382.24350.1378-0.47220.0336-1.191-1.5522-1.1403-1.1921.01620.6009-0.05541.83450.15991.2456-30.24621.999623.5492
205.2749-0.0392-0.96023.5941-2.40312.05811.07240.61730.58230.049-0.96181.4485-1.52780.308-0.12681.63140.69380.00361.5554-0.16990.984-21.276318.93895.1799
210.90330.0055-1.92144.3489-0.94014.5322-0.4443-0.8504-0.54040.22670.34120.2973-0.32890.46080.03590.4710.0626-0.0051.31140.05520.68348.53615.736-42.4071
229.6162-1.9164-1.93099.25641.03252.41631.28960.7977-2.1070.2446-0.03580.5421-0.7290.6068-1.26170.7385-0.0071-0.12771.10360.13070.69352.35075.9971-55.3524
236.4151-1.0464-7.05334.23592.94478.535-1.39050.9172-0.8902-0.2172-0.10411.40360.2482-3.59411.20980.56130.0468-0.10371.42280.15381.1278-9.0284.7777-47.3731
242.09497.20313.83259.68371.1964.28680.59671.49731.62530.70070.19290.01530.83321.5496-0.68910.5188-0.13370.01911.56420.06990.682612.61153.9376-45.7315
251.8051-1.2516-1.86776.0379-0.22856.6181-0.328-0.14420.264-0.08360.08320.0022-1.0937-0.19380.17780.48-0.0359-0.01241.08080.05550.72434.280812.934-44.551
266.89850.43192.12938.42631.21352.1459-0.3478-1.1684-0.32120.17770.2609-0.30540.6143-0.22780.05010.58760.10330.05221.39210.11640.698314.2449-6.646-32.6728
270.2327-1.18490.51364.7391-2.21011.0392-1.4546-1.85781.82370.71931.0902-0.6028-0.91850.56860.17581.3176-0.1283-0.42282.844-0.52932.208827.83717.7987-9.5748
285.8372.9193-4.11644.0685-2.00912.92431.09570.2508-0.3725-0.6159-1.04020.6225-0.314-0.843-0.35370.83980.1167-0.24842.1857-0.10851.578521.258113.1183-14.516
293.98642.66241.19042.5974-0.13211.2179-0.91840.13260.02310.09990.2305-1.3128-0.83741.37440.65331.2771-0.1327-0.12032.2119-0.02812.03832.101415.3549-17.1179
309.4957-2.23560.02112.26550.61225.8138-0.5066-0.66270.12810.9145-0.4572-0.84280.1465-0.47770.75670.97670.39060.03461.82560.25990.72920.175-7.7667-27.5506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:11)
2X-RAY DIFFRACTION2(chain A and resid 12:49)
3X-RAY DIFFRACTION3(chain A and resid 50:75)
4X-RAY DIFFRACTION4(chain A and resid 76:186)
5X-RAY DIFFRACTION5(chain A and resid 187:201)
6X-RAY DIFFRACTION6(chain A and resid 202:222)
7X-RAY DIFFRACTION7(chain A and resid 223:279)
8X-RAY DIFFRACTION8(chain A and resid 280:304)
9X-RAY DIFFRACTION9(chain A and resid 305:312)
10X-RAY DIFFRACTION10(chain A and resid 313:324)
11X-RAY DIFFRACTION11(chain B and resid 5:40)
12X-RAY DIFFRACTION12(chain B and resid 41:51)
13X-RAY DIFFRACTION13(chain B and resid 52:124)
14X-RAY DIFFRACTION14(chain B and resid 125:186)
15X-RAY DIFFRACTION15(chain B and resid 187:205)
16X-RAY DIFFRACTION16(chain B and resid 206:226)
17X-RAY DIFFRACTION17(chain B and resid 227:262)
18X-RAY DIFFRACTION18(chain B and resid 263:290)
19X-RAY DIFFRACTION19(chain B and resid 291:304)
20X-RAY DIFFRACTION20(chain B and resid 305:324)
21X-RAY DIFFRACTION21(chain C and resid 1:25)
22X-RAY DIFFRACTION22(chain C and resid 26:43)
23X-RAY DIFFRACTION23(chain C and resid 44:54)
24X-RAY DIFFRACTION24(chain C and resid 55:67)
25X-RAY DIFFRACTION25(chain C and resid 68:179)
26X-RAY DIFFRACTION26(chain C and resid 180:206)
27X-RAY DIFFRACTION27(chain C and resid 207:225)
28X-RAY DIFFRACTION28(chain C and resid 226:236)
29X-RAY DIFFRACTION29(chain C and resid 237:303)
30X-RAY DIFFRACTION30(chain C and resid 304:324)

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