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- PDB-5c5s: Crystal Structure of human Myosin 9b RhoGAP domain at 2.2 angstrom -

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Basic information

Entry
Database: PDB / ID: 5c5s
TitleCrystal Structure of human Myosin 9b RhoGAP domain at 2.2 angstrom
ComponentsUnconventional myosin-IXb
KeywordsSIGNALING PROTEIN / RhoGAP domain
Function / homology
Function and homology information


Roundabout binding / lamellipodium morphogenesis / actin filament-based movement / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / regulation of Rho protein signal transduction / RHOF GTPase cycle / myosin complex / regulation of small GTPase mediated signal transduction / microfilament motor activity ...Roundabout binding / lamellipodium morphogenesis / actin filament-based movement / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / regulation of Rho protein signal transduction / RHOF GTPase cycle / myosin complex / regulation of small GTPase mediated signal transduction / microfilament motor activity / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / ruffle / RAC1 GTPase cycle / GTPase activator activity / actin filament / ADP binding / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell cortex / calmodulin binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Unconventional myosin-IXb / Class IX myosin, motor domain / : / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...Unconventional myosin-IXb / Class IX myosin, motor domain / : / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / IQ calmodulin-binding motif / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Zinc finger phorbol-ester/DAG-type signature. / IQ motif profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / IQ motif, EF-hand binding site / C1-like domain superfamily / Kinesin motor domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unconventional myosin-IXb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYi, F.S. / Ren, J.Q. / Feng, W.
CitationJournal: J.Clin.Invest. / Year: 2015
Title: Myo9b is a key player in SLIT/ROBO-mediated lung tumor suppression
Authors: Kong, R. / Yi, F. / Wen, P. / Liu, J. / Chen, X. / Ren, J. / Li, X. / Shang, Y. / Nie, Y. / Wu, K. / Fan, D. / Zhu, L. / Feng, W. / Wu, J.Y.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-IXb
B: Unconventional myosin-IXb
C: Unconventional myosin-IXb
D: Unconventional myosin-IXb


Theoretical massNumber of molelcules
Total (without water)104,2414
Polymers104,2414
Non-polymers00
Water6,359353
1
A: Unconventional myosin-IXb


Theoretical massNumber of molelcules
Total (without water)26,0601
Polymers26,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Unconventional myosin-IXb


Theoretical massNumber of molelcules
Total (without water)26,0601
Polymers26,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Unconventional myosin-IXb


Theoretical massNumber of molelcules
Total (without water)26,0601
Polymers26,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Unconventional myosin-IXb


Theoretical massNumber of molelcules
Total (without water)26,0601
Polymers26,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.084, 84.984, 134.139
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Unconventional myosin-IXb / Unconventional myosin-9b


Mass: 26060.262 Da / Num. of mol.: 4 / Fragment: UNP residues 1691-1916
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO9B, MYR5 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13459
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M NH4Ac, 0.1 M Bis-Tris and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45424 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.113 / Net I/av σ(I): 10.5 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OW3

1ow3


Resolution: 2.2→39.57 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 1995 4.4 %Random selection
Rwork0.2214 43350 --
obs0.2225 45345 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.81 Å2 / Biso mean: 52.6595 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 2.2→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 0 353 6770
Biso mean---46.77 -
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036598
X-RAY DIFFRACTIONf_angle_d0.7068947
X-RAY DIFFRACTIONf_chiral_restr0.0251049
X-RAY DIFFRACTIONf_plane_restr0.0031145
X-RAY DIFFRACTIONf_dihedral_angle_d13.792520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1997-2.25470.34011390.28763029316899
2.2547-2.31570.34361410.278130423183100
2.3157-2.38380.31241400.281530723212100
2.3838-2.46080.34331410.306330503191100
2.4608-2.54870.34161410.27430753216100
2.5487-2.65070.31321420.273330523194100
2.6507-2.77130.31871410.251130713212100
2.7713-2.91740.31521430.276230893232100
2.9174-3.10010.26671420.257830973239100
3.1001-3.33940.30721430.243130813224100
3.3394-3.67520.21671440.225131213265100
3.6752-4.20650.20871430.189531153258100
4.2065-5.29770.21471450.168731663311100
5.2977-39.57670.16111500.17473290344099
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)
15.204-0.62171.05924.2195-1.71945.3606-0.04770.1235-0.3449-0.02220.08590.53450.3215-0.5688-0.0390.2854-0.0437-0.00530.239-0.05830.3116-12.980139.890818.0667
21.01820.7183-0.65516.0016-2.76534.83440.04480.18080.0493-0.0696-0.1983-0.1874-0.150.36310.12950.131-0.013-0.00810.2439-0.01090.22280.821452.405912.4433
33.02750.7321-0.40865.8832.81777.0460.04480.09360.00690.0314-0.17470.01850.01250.44890.19530.19830.0048-0.04390.16380.03620.36875.171552.204813.9902
47.96880.6173.50937.3592-0.48335.9553-0.1339-0.68110.71470.4430.2466-0.7187-0.72871.30520.07780.2884-0.10820.04890.6885-0.17540.468915.582843.696845.121
56.4283-1.66444.8737.6816-3.74178.65430.3502-0.2836-0.39160.37090.26940.75570.9279-0.2192-0.6160.30480.01010.01150.21360.05680.3314-2.358934.954543.0636
67.49174.0531-4.17587.345-4.75887.8988-0.03820.0031-0.9772-0.5211-0.4403-1.14061.12781.14040.41250.47080.1905-0.0270.4382-0.00830.622714.673129.942245.1187
75.2799-2.9866-2.66553.81174.72066.5232-0.2833-0.97380.35050.58560.8228-0.5154-0.43160.9468-0.59310.6123-0.0042-0.00520.4472-0.00890.32995.669147.539956.3445
82.02590.02290.48266.10152.76636.6079-0.0711-0.3150.2040.21530.18110.0266-1.29890.1453-0.10160.57290.01170.08960.3110.00530.33810.61350.992150.9072
95.55241.34060.65497.5204-3.71493.1895-0.19770.08890.2461-0.1813-0.03930.2674-1.1371-0.52330.2620.74090.09630.04790.24440.0080.414-3.692354.779545.2422
107.48693.2281-5.25563.5442-2.86546.85050.2111-1.23620.95352.35030.23620.0414-1.66681.4033-0.50840.67610.0642-0.090.4851-0.15760.4309-1.527660.360921.05
117.07073.2982.08928.2804-1.94642.29290.3728-0.01860.5809-0.6206-0.56442.0944-1.407-1.79320.22460.62140.2113-0.07330.60980.00230.676618.359548.016917.1949
127.11820.1554.78797.71170.647.15470.42640.0195-0.44220.5147-0.06570.19470.8385-0.143-0.30370.3829-0.0322-0.02430.2238-0.00330.291534.865641.348825.7116
132.899-3.05972.43549.4573-0.93888.79880.8719-0.1283-2.50740.05120.06270.92741.571-0.7828-0.90130.764-0.2142-0.30170.52960.09391.042425.586732.391721.4966
144.55120.35021.18038.5513-5.24327.90070.1740.6663-0.1908-0.52170.07360.33650.28670.1748-0.25660.29410.119-0.01940.385-0.0850.251132.776651.091510.8103
158.32575.5597-5.84396.6268-3.74624.14850.38990.32260.98430.4281-0.16650.4972-1.47780.6126-0.15480.72010.03070.05320.61660.19570.480834.920265.726113.7923
167.2872-2.19633.33934.3522-2.31028.36510.0450.13570.05940.22340.06210.1483-0.1397-0.0784-0.11720.24860.00160.01950.1337-0.01450.296736.956750.552819.6219
175.6333-0.84810.41337.71460.30861.94610.02340.1322-0.05640.4776-0.10080.1308-0.04150.38480.11020.2840.02830.0240.23010.07410.374540.608757.822418.8032
188.9486-4.5672-4.22874.55455.54378.20681.47591.02061.0745-2.25370.0454-0.6321-3.0404-0.4383-1.471.00930.04880.08730.6408-0.00150.384438.473664.073546.2077
198.67611.61942.16176.99530.7846.9047-0.129-0.37410.32470.0296-0.1386-0.31590.20320.85630.23190.27050.1110.03220.39870.05380.309548.85947.133747.5679
203.8071-1.7075-1.993.00091.67473.1975-0.5344-0.678-0.2250.8010.5035-0.68290.90661.36850.00310.56980.2098-0.06120.5980.06420.463151.796644.275652.6733
212.1092-1.2927-0.89965.61422.32527.17110.0966-0.2628-0.01960.2742-0.1640.2372-0.4305-0.79080.060.25590.04620.02270.39570.05280.240335.613155.726853.224
222.8411-0.12320.39693.8554-0.61479.35990.1756-0.11540.00870.1145-0.03770.0826-0.0846-0.7317-0.1530.20180.03840.040.28760.00260.399632.823855.493452.9505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 196 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 273 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 318 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 114 through 145 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 146 through 158 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 159 through 182 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 217 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 287 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 288 through 314 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 315 through 319 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 114 through 132 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 133 through 158 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 159 through 182 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 183 through 218 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 219 through 234 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 235 through 276 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 277 through 314 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 315 through 319 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 116 through 160 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 161 through 206 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 207 through 273 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 274 through 318 )D0

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