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- PDB-6cds: Human neurofibromin 2/merlin/schwannomin residues 1-339 in comple... -

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Basic information

Entry
Database: PDB / ID: 6cds
TitleHuman neurofibromin 2/merlin/schwannomin residues 1-339 in complex with PIP2
ComponentsMerlin
KeywordsSIGNALING PROTEIN / NEUROFIBROMIN 2 / SCHWANNOMIN / merlin / Tumor Suppressor protein
Function / homology
Function and homology information


regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome ...regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / cell-cell junction organization / regulation of protein localization to nucleus / filopodium membrane / negative regulation of MAPK cascade / cortical actin cytoskeleton / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / RHO GTPases activate PAKs / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / positive regulation of stress fiber assembly / negative regulation of cell migration / filopodium / hippocampus development / positive regulation of cell differentiation / adherens junction / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / MAPK cascade / integrin binding / apical part of cell / lamellipodium / actin binding / cell body / regulation of cell shape / actin cytoskeleton organization / regulation of apoptotic process / early endosome / cytoskeleton / regulation of cell cycle / neuron projection / negative regulation of cell population proliferation / nucleolus / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-PIO / PHOSPHATE ION / Merlin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsChinthalapudi, K. / Sharff, A.J. / Bricogne, G. / Izard, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS077952 United States
CitationJournal: Nat Commun / Year: 2018
Title: Lipid binding promotes the open conformation and tumor-suppressive activity of neurofibromin 2.
Authors: Chinthalapudi, K. / Mandati, V. / Zheng, J. / Sharff, A.J. / Bricogne, G. / Griffin, P.R. / Kissil, J. / Izard, T.
History
DepositionFeb 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Merlin
B: Merlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3469
Polymers80,3592
Non-polymers1,9877
Water3,999222
1
A: Merlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1274
Polymers40,1801
Non-polymers9483
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Merlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2195
Polymers40,1801
Non-polymers1,0404
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.310, 96.590, 106.450
Angle α, β, γ (deg.)90.00, 99.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Merlin / / Moesin-ezrin-radixin-like protein / Neurofibromin-2 / Schwannomerlin / Schwannomin


Mass: 40179.520 Da / Num. of mol.: 2 / Mutation: G302E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF2, SCH / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: P35240

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES (pH 7.5), 50 mM MgCl2(H2O)6, 35 % PEG 550 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 14, 2015
Details: sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→96.92 Å / Num. obs: 23131 / % possible obs: 99.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 56.49 Å2 / CC1/2: 0.984 / Rpim(I) all: 0.119 / Net I/σ(I): 5.5
Reflection shellResolution: 2.71→2.84 Å / Redundancy: 3.6 % / Num. unique obs: 2952 / CC1/2: 0.31 / Rpim(I) all: 0.971 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.13.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1isn

1isn


Resolution: 2.62→48.3 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.367
Details: THE RESIDUE RANGES FOR EACH OF THE 8 TLS DOMAINS ARE AS FOLLOWS: TLS DOMAIN 1: A15 - A103 AND A804, A810, A813, A814, A820, A825, A829, A831, A832, A834, A835, A1004, A1005, A1017, A1020, ...Details: THE RESIDUE RANGES FOR EACH OF THE 8 TLS DOMAINS ARE AS FOLLOWS: TLS DOMAIN 1: A15 - A103 AND A804, A810, A813, A814, A820, A825, A829, A831, A832, A834, A835, A1004, A1005, A1017, A1020, A1023, A1027, A1032, A1038, A1039, A1042, A1050, A1053, A1058, A1060, A1062, A1067, A1068, A1071, A1072 TLS DOMAINS 2: A104 - A219 AND A656, A803, A806, A807, A809, A815, A816, A818, A821, A823, A830, A838, A839, A840, A1002, A1003, A1006, A1007, A1009, A1025, A1029, A1030, A1031, A1033, A1034, A1035, A1037, A1046, A1048, B1049, A1051, A1054, A1059, A1063 TLS DOMAIN 3: A220 - A290 AND A801, A805, A811, A812, A817, A822, A827, A833, A836, A837, A1010, A1011, A1013, A1021, A1024, A1026, A1028, A1040, A1041, A1047, A1052, A1055, A1057, A1061, A1064, A1065, A1066, A1070 TLS DOMAIN 4: A291 - A339 AND A500, A690, A802, A808, A819, A824, A826, A828, A1001, A1008, A1012, A1022, A1036, A1043, A1044, A1045, A1056, A1069 TLS DOMAIN 5: B15 - B103 AND A804, B810, B813, B814, B820, B825, B829, B831, B832, B834, B835, B1073, B1075, B1079, B1082, B1084, B1091, B1092, B1093, B1100, B1101, B1105, B1112, B1120, B1133, B1134, B1138 TLS DOMAIN 6: B104 - B219 AND B641, B803, B806, B807, B815, B816, B818, B821, B823, B830, B834, B838, B839, B1074, B1076, B1080, B1081, B1083, B1086, B1087, B1088, B1096, B1098, B1104, B1107, B1110, B1111, B1113, B1114, B1115, B1117, B1118, B1122, B1123, B1124, B1125, B1127, B1128, B1137, B1139, B1140 TLS DOMAIN 7: B220 - B290 AND B671, B700, B801, B805, B809, B811, B812, B817, B822, B827, B833, B836, B837, B8105, B1089, B1090, B1094, B9105, B1099, B1103, B1108, B1109, B1116, B1129, B1130, B1131, B1132, B1136, B1142, B1143 TLS DOMAIN 8: B291 - B339 AND B500, B802, B808, B819, B824, B826, B828, B1077, B1078, B1097, B1102, B1106, B1119, B1121, B1126, B1135, B1141
RfactorNum. reflection% reflectionSelection details
Rfree0.237 962 5.01 %RANDOM
Rwork0.188 ---
obs0.191 19196 74.8 %-
Displacement parametersBiso mean: 42.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.891 Å20 Å2-0.0067 Å2
2---4.3037 Å20 Å2
3---5.1947 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.62→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5395 0 96 222 5713
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0619970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1685HARMONIC5
X-RAY DIFFRACTIONt_it11037HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion16.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion705SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11748SEMIHARMONIC4
LS refinement shellResolution: 2.62→2.76 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4045 -7.06 %
Rwork0.2658 250 -
all0.2746 269 -
obs--7.23 %
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)
11.3811.02931.29254.13561.66630.9720.03550.0871-0.19970.12940.1196-0.362-0.1462-0.0597-0.1551-0.07580.05040.0179-0.1351-0.03840.076616.600757.798854.3115
20.1898-0.9102-0.59442.10370.98680.19870.0562-0.09920.0466-0.351-0.09130.14-0.0469-0.28240.0351-0.01240.0739-0.077-0.0657-0.02450.05430.609645.258234.0631
3-0.06950.0870.20351.1764-0.08230.10150.02470.0287-0.12240.11030.1118-0.26530.31610.2048-0.1364-0.08120.02570.0489-0.06290.02390.130816.929628.035856.4705
40.27840.1762-0.85980.16240.1030.24870.0578-0.1657-0.01230.0295-0.0663-0.046-0.1413-0.02840.0085-0.16730.00040.04610.0904-0.08140.0694-7.122241.735565.2907
51.8271-2.1225-0.56293.79190.85031.26620.0223-0.00930.0717-0.14240.0634-0.4911-0.0015-0.1174-0.0857-0.1098-0.03870.011-0.167-0.02740.150325.03746.0066-2.2262
60.4650.3742-0.1590.69931.4482.3166-0.14640.1329-0.02270.2715-0.01780.1040.1407-0.13090.16410.0269-0.03950.0326-0.1399-0.00180.04788.873118.578717.742
7-0.1249-0.11760.73691.3377-0.01210.4831-0.0540.2138-0.0420.09080.0548-0.3761-0.24960.1243-0.0008-0.1139-0.0561-0.0658-0.06430.03660.123625.208135.6451-4.2806
80.413-0.24940.19170.08860.46640.05180.0240.31570.014-0.0169-0.095-0.09840.02710.00830.071-0.1155-0.0007-0.01930.06590.00650.04641.901122.3883-13.3776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1domain1
2X-RAY DIFFRACTION2domain2
3X-RAY DIFFRACTION3domain3
4X-RAY DIFFRACTION4domain4
5X-RAY DIFFRACTION5domain5
6X-RAY DIFFRACTION6domain6
7X-RAY DIFFRACTION7domain7
8X-RAY DIFFRACTION8domain8

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