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- PDB-3m3w: Crystal structure of mouse PACSIN3 BAR domain mutant -

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Basic information

Entry
Database: PDB / ID: 3m3w
TitleCrystal structure of mouse PACSIN3 BAR domain mutant
ComponentsProtein kinase C and casein kinase II substrate protein 3
KeywordsENDOCYTOSIS / Mouse / PACSIN3 / BAR domain
Function / homology
Function and homology information


plasma membrane tubulation / Clathrin-mediated endocytosis / negative regulation of endocytosis / positive regulation of membrane protein ectodomain proteolysis / negative regulation of calcium ion transport / regulation of endocytosis / calcium channel inhibitor activity / cytoskeleton organization / cytoskeletal protein binding / phospholipid binding ...plasma membrane tubulation / Clathrin-mediated endocytosis / negative regulation of endocytosis / positive regulation of membrane protein ectodomain proteolysis / negative regulation of calcium ion transport / regulation of endocytosis / calcium channel inhibitor activity / cytoskeleton organization / cytoskeletal protein binding / phospholipid binding / endocytosis / endosome / lipid binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains ...Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein kinase C and casein kinase II substrate protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMeng, G. / Bai, X.Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Rigidity of wedge loop in PACSIN 3 protein is a key factor in dictating diameters of tubules
Authors: Bai, X.Y. / Meng, G. / Luo, M. / Zheng, X.F.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Mar 5, 2014Group: Database references
Revision 1.4Sep 9, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C and casein kinase II substrate protein 3
B: Protein kinase C and casein kinase II substrate protein 3


Theoretical massNumber of molelcules
Total (without water)74,6962
Polymers74,6962
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-63 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.494, 52.265, 196.461
Angle α, β, γ (deg.)90.00, 94.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein kinase C and casein kinase II substrate protein 3 / PACSIN3


Mass: 37347.824 Da / Num. of mol.: 2 / Fragment: BAR domain, residues 1-320 / Mutation: E128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99JB8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.25 Å3/Da / Density % sol: 62.19 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 29998 / Num. obs: 28370 / % possible obs: 94.6 % / Observed criterion σ(I): 3
Reflection shellResolution: 2.6→2.63 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.858 / SU B: 19.182 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28058 1492 5 %RANDOM
Rwork0.23222 ---
obs0.2346 28282 99.76 %-
all-29998 --
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: 50.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.31 Å2
2--0.04 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4550 0 0 10 4560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214690
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9236311
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49722.863255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11615810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211553
X-RAY DIFFRACTIONr_chiral_restr0.1030.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023671
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22021
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23125
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.52904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it024452
X-RAY DIFFRACTIONr_scbond_it032054
X-RAY DIFFRACTIONr_scangle_it04.51859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 97 -
Rwork0.239 2010 -
obs--99.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.5442-1.0244-2.90710.56273.449924.2460.1547-0.66360.63930.79840.0480.3538-1.24170.055-0.20260.4203-0.05840.04010.2777-0.04710.1555-18.65451.3657128.2509
28.7934-0.3563-6.02592.0105-3.088526.31010.1324-0.24870.64130.3966-0.11020.2705-1.14720.1566-0.02230.3265-0.0016-0.00060.0778-0.05260.2001-16.74252.5057115.4173
36.28381.9175-6.09234.3765-2.92418.61420.14740.09560.19550.3120.0350.0199-0.5306-0.2456-0.18230.11410.0276-0.11450.0491-0.02550.0602-5.40044.752396.5389
410.83245.6274-13.5173.3435-5.751620.70940.12080.72420.60310.0646-0.02-0.0118-0.5365-0.6733-0.10080.1260.0285-0.04120.09080.01830.110810.39566.304977.1955
56.5611-0.1824-6.8086.5221-0.19577.087-0.08720.6681-0.1429-1.2954-0.29440.00130.07220.07470.38160.351-0.03830.02740.3266-0.0660.261220.48290.567765.531
610.5967-1.2034-6.83650.85731.33974.8510.08420.6785-0.0793-0.3896-0.1067-0.01180.087-0.44340.02260.1680.00470.00030.16950.01730.14128.6709-2.032776.521
729.8988-2.3246-16.02371.59275.841423.5452-0.12160.8789-0.4838-0.3924-0.18120.2074-0.4096-0.41610.30280.108-0.0206-0.03940.09980.00310.1404-6.3572-0.602887.4586
810.2019-2.48271.34499.7548-3.05663.5490.20790.03340.0298-0.50810.09120.2887-0.8565-0.509-0.29910.15010.0138-0.04710.1346-0.02140.0598-17.0622-0.631396.6875
97.78260.2259-5.18850.0066-0.15063.45910.42953.29370.74491.9528-0.32681.7672-3.3332-0.5766-0.10260.90850.6985-0.21821.0812-0.08170.8114-25.79362.8799107.6709
102.9301-1.2486-3.0081.44553.884510.504-0.0905-0.06120.13310.50960.13870.5995-1.5246-1.1047-0.04820.62010.04760.09590.42660.01440.2985-28.75671.2029127.5983
110.54851.62595.11387.519318.362551.4783-0.1195-0.52841.10280.4348-0.0802-0.156-1.4555-0.20160.19961.2166-0.00930.2190.8893-0.17340.5752-25.75367.9733151.0325
123.77742.2206-1.374.55486.364116.3156-0.1054-1.21130.36460.2777-0.5979-0.4872-1.3934-0.2660.70331.94850.14760.1121.4352-0.05410.6808-26.804813.0154170.4979
132.7107-2.0857-5.828623.903127.106935.4836-0.043-0.24380.06931.4683-0.73720.69931.1745-1.6930.78021.06560.02120.27240.7599-0.05780.243-29.1536-3.8663145.3329
143.1902-0.3525-3.95152.21749.920346.18040.1588-0.1129-0.99460.032-0.59610.23781.3687-1.30110.43730.4446-0.05990.07660.3053-0.12240.4-25.8505-8.2287127.8284
153.8198-3.4641.81157.16746.94919.1935-0.1322-0.242-0.26090.4856-0.08580.51480.4162-0.74480.2180.2229-0.0647-0.01240.09020.00030.1528-19.2682-8.104115.389
166.47282.71192.637510.503-7.955423.9303-0.1469-0.05650.4012-0.1018-0.08420.2674-0.574-0.5950.23110.03840.0335-0.0334-0.0121-0.04120.0809-13.7106-6.7107105.4627
172.7973-0.6092-0.17562.33441.65565.3367-0.26480.4095-0.5159-0.29240.01280.1120.2706-0.11120.25190.0656-0.0045-0.04010.02580.00510.0787-3.4852-8.380795.3584
1821.822211.0576-16.11587.6419-2.870425.6568-0.63690.6687-1.6491-0.3121-0.0520.17661.3481-0.08740.68890.22880.0085-0.00420.0912-0.09210.34838.2941-11.733882.198
1916.29491.0044-13.01750.14850.051718.8233-0.7995-0.2725-1.3782-0.66710.0247-0.3651.15830.68920.77480.41790.05710.22320.27920.02390.645923.3261-11.139468.7608
208.0631.4916-4.05342.0943-3.004921.5939-0.66411.1954-0.4571-1.056-0.1447-0.1590.4823-0.44710.80880.7624-0.07360.2130.7601-0.20030.581131.9981-3.553142.8158
2113.79970.66233.0340.2976-0.1480.9914-0.39751.67610.638-1.10320.1082-0.224-0.6851-0.08730.28930.6421-0.05840.12120.7183-0.07030.413834.74093.911749.5949
221.4943-1.8692-0.18912.34780.45785.07810.43610.7549-0.3433-0.417-0.4559-0.5134-0.29360.52640.01980.2444-0.00150.05540.41260.05190.361529.12366.470269.0595
2317.6861-10.9192-12.637111.41049.69059.79330.3307-0.28180.404-0.2592-0.0659-0.3587-0.50520.6077-0.26480.093-0.0082-0.06790.18920.05850.125817.0566.566683.6522
248.9019-2.6192-10.15492.70354.800513.28410.3047-0.33150.53110.0442-0.063-0.2024-0.7020.892-0.24170.1558-0.0296-0.08510.10110.01650.12315.58986.352298.8257
256.33465.1014-4.934218.316-0.40616.13980.441-0.5329-0.00120.8629-0.3113-0.3642-0.58780.2753-0.12970.25220.0177-0.07420.1384-0.00630.08-4.4091.4447111.5418
263.0247-1.97-2.12181.71870.778710.721-0.0494-0.61410.12710.2322-0.11660.12150.01930.19850.1660.08670.0015-0.05390.04990.02040.04250.8362-2.6194104.9169
278.4381.8003-5.41816.8678-3.00937.3951-0.0789-0.7585-0.47630.5236-0.3792-0.4553-0.17580.70250.45810.1317-0.0099-0.10850.1730.03710.158716.15730.500394.2115
2814.89490.5653-11.22623.35692.819111.61840.3661-0.8071-0.0472-0.0329-0.4934-0.5309-0.36520.96540.12730.19520.0467-0.0270.46980.21510.394930.50113.399281.5403
2915.184314.4622-13.369514.3698-11.018416.7141.0368-2.1758-2.6097-0.0928-1.7399-2.4229-0.73721.08310.70310.32350.0531-0.02010.65850.31850.718642.66958.841971.902
305.110511.4811-4.708725.7929-10.57844.33850.5679-0.7146-1.37530.5246-0.0937-1.4967-1.1380.3663-0.47420.404-0.0908-0.08570.52760.17020.299843.260511.394764.6063
315.15333.3758-6.07712.486-6.946539.18910.20360.60610.7047-1.30920.2142-0.7313-1.0130.4258-0.41780.7945-0.03090.18080.8021-0.13910.463144.76775.787148.9657
3211.0878-10.68160.088925.3403-5.6898.26420.67861.82650.0319-2.62570.01470.9239-0.82850.4839-0.69341.5351-0.09810.22781.4587-0.05850.563541.79868.141929.0677
338.76765.80171.28119.45283.70851.6450.99340.1647-0.04770.75650.76430.5272-1.24241.0507-1.75782.1134-0.01550.11971.8526-0.01330.991334.224314.01665.2198
349.6856-21.221224.981946.4958-54.735564.43550.54580.0923-0.9463-1.57230.43233.03952.0584-1.5665-0.97811.8621-0.23160.03581.905-0.11171.495144.82327.03213.5691
354.76750.3545-7.99662.3398-4.865428.8495-0.43330.2897-0.3706-0.83980.0594-0.55161.56651.24170.37390.7369-0.01230.22270.7314-0.07260.626942.4426-3.863948.6145
3612.40690.1609-7.91492.33-1.2835.6478-0.43540.0774-0.7449-0.3466-0.2617-0.44430.41560.03260.69710.17730.03360.01270.25270.05090.330524.52-5.78578.6107
3726.06512.0468-19.11567.5011-6.707223.9755-0.3226-0.5313-1.3530.339-0.4214-1.51041.34011.39940.74410.22030.0558-0.07240.1180.04850.341911.3645-11.290495.6828
389.41031.714-11.73355.3648-3.260219.094-0.41780.0789-0.67640.2345-0.11710.01761.3073-0.14990.53490.15880.0191-0.08730.07640.06050.1376-3.362-12.3713107.6803
394.4215-1.1051-4.46611.23924.440920.3984-0.0852-0.6585-0.01950.6315-0.22410.18050.01710.43350.30930.2554-0.0322-0.01830.1975-0.01460.1413-11.9116-6.0475123.959
4015.38199.87181.945212.49148.02447.70470.6328-1.70110.20022.0736-1.17040.77611.04770.66590.53771.02440.09470.08450.6809-0.05790.4207-18.5776-1.2107145.3081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 23
2X-RAY DIFFRACTION2A24 - 32
3X-RAY DIFFRACTION3A33 - 52
4X-RAY DIFFRACTION4A53 - 64
5X-RAY DIFFRACTION5A65 - 81
6X-RAY DIFFRACTION6A82 - 96
7X-RAY DIFFRACTION7A97 - 106
8X-RAY DIFFRACTION8A107 - 115
9X-RAY DIFFRACTION9A116 - 119
10X-RAY DIFFRACTION9A125 - 129
11X-RAY DIFFRACTION10A130 - 147
12X-RAY DIFFRACTION11A148 - 163
13X-RAY DIFFRACTION12A164 - 180
14X-RAY DIFFRACTION12A184 - 202
15X-RAY DIFFRACTION13A203 - 218
16X-RAY DIFFRACTION14A219 - 227
17X-RAY DIFFRACTION15A228 - 236
18X-RAY DIFFRACTION16A237 - 242
19X-RAY DIFFRACTION17A243 - 255
20X-RAY DIFFRACTION18A256 - 266
21X-RAY DIFFRACTION19A267 - 281
22X-RAY DIFFRACTION20A282 - 301
23X-RAY DIFFRACTION21B14 - 27
24X-RAY DIFFRACTION22B28 - 42
25X-RAY DIFFRACTION23B43 - 52
26X-RAY DIFFRACTION24B53 - 66
27X-RAY DIFFRACTION25B67 - 76
28X-RAY DIFFRACTION26B77 - 88
29X-RAY DIFFRACTION27B89 - 100
30X-RAY DIFFRACTION28B101 - 114
31X-RAY DIFFRACTION29B115 - 122
32X-RAY DIFFRACTION30B123 - 128
33X-RAY DIFFRACTION31B129 - 145
34X-RAY DIFFRACTION32B146 - 157
35X-RAY DIFFRACTION33B158 - 183
36X-RAY DIFFRACTION34B187 - 208
37X-RAY DIFFRACTION35B209 - 238
38X-RAY DIFFRACTION36B239 - 256
39X-RAY DIFFRACTION37B257 - 267
40X-RAY DIFFRACTION38B268 - 280
41X-RAY DIFFRACTION39B281 - 294
42X-RAY DIFFRACTION40B295 - 302

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