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- PDB-4f93: Brr2 Helicase Region S1087L, Mg-ATP -

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Basic information

Entry
Database: PDB / ID: 4f93
TitleBrr2 Helicase Region S1087L, Mg-ATP
ComponentsU5 small nuclear ribonucleoprotein 200 kDa helicase
KeywordsHYDROLASE / RNP remodeling / pre-mRNA splicing / spliceosome catalytic activation / DEXD/H-box RNA Helicase / RNA and ATP binding / Nucleus
Function / homology
Function and homology information


cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / cilium / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / C2 domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / SULFANILAMIDE / U5 small nuclear ribonucleoprotein 200 kDa helicase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsSantos, K.F. / Jovin, S.M. / Weber, G. / Pena, V. / Luehrmann, R. / Wahl, M.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for functional cooperation between tandem helicase cassettes in Brr2-mediated remodeling of the spliceosome.
Authors: Santos, K.F. / Jovin, S.M. / Weber, G. / Pena, V. / Luhrmann, R. / Wahl, M.C.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,3955
Polymers197,2641
Non-polymers1,1314
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.120, 154.586, 143.280
Angle α, β, γ (deg.)90.00, 120.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules B

#1: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 197264.312 Da / Num. of mol.: 1 / Fragment: Brr2 Helicase Region / Mutation: S1087L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP200, ASCC3L1, HELIC2, KIAA0788 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75643, RNA helicase

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Non-polymers , 5 types, 55 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SAN / SULFANILAMIDE


Mass: 172.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O2S / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.55 Å3/Da / Density % sol: 65.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate, 1.2 M sodium Malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. all: 58752 / Num. obs: 58458 / % possible obs: 99.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 2.92→3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.52 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→47.363 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2917 4.99 %Random
Rwork0.1972 ---
obs0.1997 58458 98.06 %-
all-58752 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89.204 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6465 Å20 Å2-12.2888 Å2
2--32.3919 Å20 Å2
3----33.0383 Å2
Refinement stepCycle: LAST / Resolution: 2.92→47.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13856 0 70 51 13977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614235
X-RAY DIFFRACTIONf_angle_d1.00819304
X-RAY DIFFRACTIONf_dihedral_angle_d18.6275369
X-RAY DIFFRACTIONf_chiral_restr0.0682187
X-RAY DIFFRACTIONf_plane_restr0.0042459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.97120.40621270.35952414X-RAY DIFFRACTION89
2.9712-3.02240.35981380.31842633X-RAY DIFFRACTION99
3.0224-3.07740.40511390.30862658X-RAY DIFFRACTION99
3.0774-3.13660.35631390.29852695X-RAY DIFFRACTION99
3.1366-3.20060.37321400.28452654X-RAY DIFFRACTION99
3.2006-3.27010.35511400.28062651X-RAY DIFFRACTION99
3.2701-3.34620.3421430.26132703X-RAY DIFFRACTION99
3.3462-3.42990.31891380.25512632X-RAY DIFFRACTION99
3.4299-3.52260.31851400.24742662X-RAY DIFFRACTION99
3.5226-3.62620.28321380.2212655X-RAY DIFFRACTION99
3.6262-3.74320.24781390.19712652X-RAY DIFFRACTION99
3.7432-3.87690.26331400.19522648X-RAY DIFFRACTION98
3.8769-4.03210.23591370.19882601X-RAY DIFFRACTION97
4.0321-4.21550.2991380.18492620X-RAY DIFFRACTION97
4.2155-4.43750.22241380.17262626X-RAY DIFFRACTION97
4.4375-4.71530.23021380.15732625X-RAY DIFFRACTION98
4.7153-5.0790.18181390.15542662X-RAY DIFFRACTION98
5.079-5.58940.22881410.18492681X-RAY DIFFRACTION99
5.5894-6.39650.281410.21492685X-RAY DIFFRACTION99
6.3965-8.05250.24211420.18962695X-RAY DIFFRACTION99
8.0525-47.36930.16831420.1592689X-RAY DIFFRACTION97
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)
11.62570.7678-0.35831.1289-0.61541.94440.20020.24490.4664-0.2286-0.3003-0.3678-0.47780.80280.00011.373-0.3529-0.15991.16790.00291.2401-5.606916.2838-40.6325
23.3189-0.20890.32464.45620.23844.97110.1016-0.2550.6331-0.185-0.23830.8784-0.7614-0.07030.00410.9433-0.34180.02020.5233-0.11811.0661-24.959514.2172-38.6643
32.50180.57840.03011.6978-0.22721.8394-0.1193-0.61650.30540.46280.1103-0.2835-0.98770.7230.00741.3115-0.7259-0.2051.4387-0.09190.941-0.867720.6499-18.871
41.6668-0.64370.02722.3307-0.91362.5386-0.05320.405-0.213-0.18710.2333-0.06160.80580.6299-0.00030.9199-0.1215-0.08840.7494-0.09070.783-20.1874-11.048-41.7642
53.81720.3347-0.12942.6308-0.05594.1404-0.0971-0.95480.02560.47570.0458-0.21250.51970.79790.00030.72560.0579-0.0840.75020.03320.667-20.962-9.2058-9.8846
60.7714-0.23720.50090.74350.23640.5654-0.2274-0.7790.28570.2269-0.115-0.0017-0.00830.23460.00081.139-0.14650.19081.498-0.47351.2009-38.93347.268.1344
74.17881.64810.98441.329-0.50793.65380.2329-0.84150.3530.267-0.31420.34970.3553-0.26860.00360.7197-0.19090.06930.6789-0.02060.8121-51.7944-9.5941-11.0739
82.9329-1.1162-0.46312.4334-0.08263.409-0.04910.8388-0.1535-0.23630.04030.36130.7818-1.3366-0.00720.888-0.90070.00381.1469-0.08190.7623-79.8178-22.5611-42.1684
93.71440.9089-0.73911.4477-0.52926.80490.01360.04040.0348-0.1431-0.0457-0.0460.193-0.6474-0.00340.6026-0.22340.05540.44520.0110.734-53.1371-8.51-44.3006
102.0535-0.1602-0.68072.33650.73570.989-0.3740.11110.22360.40770.26930.31870.2811-0.8244-0.03050.8945-0.52270.21691.47640.1631.0193-85.4812-12.6235-16.4752
111.9640.23970.13452.0855-0.34111.61860.17120.09970.6593-0.23290.4668-0.0557-0.1686-0.29640.00010.991-0.08790.16031.26420.20821.3915-77.127414.5015-30.0053
120.2008-0.11820.15050.07-0.08750.1126-0.45020.25660.1588-1.01480.50860.5408-0.0517-0.39560.00062.2638-0.0644-0.00422.47630.49781.7788-84.572527.0987-55.8616
130.61550.8637-0.53791.2107-0.7530.46920.26581.03120.6313-0.17940.02050.66290.2114-0.753401.24170.1385-0.08372.16560.4331.6775-103.023217.1061-37.4661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B AND RESSEQ 403:486)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 487:683)
3X-RAY DIFFRACTION3(CHAIN B AND RESSEQ 684:888)
4X-RAY DIFFRACTION4(CHAIN B AND RESSEQ 889:993)
5X-RAY DIFFRACTION5(CHAIN B AND RESSEQ 994:1125)
6X-RAY DIFFRACTION6(CHAIN B AND RESSEQ 1126:1181)
7X-RAY DIFFRACTION7(CHAIN B AND RESSEQ 1182:1294)
8X-RAY DIFFRACTION8(CHAIN B AND RESSEQ 1295:1521)
9X-RAY DIFFRACTION9(CHAIN B AND RESSEQ 1522:1724)
10X-RAY DIFFRACTION10(CHAIN B AND RESSEQ 1725:1824)
11X-RAY DIFFRACTION11(CHAIN B AND RESSEQ 1825:1957)
12X-RAY DIFFRACTION12(CHAIN B AND RESSEQ 1958:2014)
13X-RAY DIFFRACTION13(CHAIN B AND RESSEQ 2015:2125)

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