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- PDB-4kit: Crystal structure of human Brr2 in complex with the Prp8 Jab1/MPN... -

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Basic information

Entry
Database: PDB / ID: 4kit
TitleCrystal structure of human Brr2 in complex with the Prp8 Jab1/MPN domain
Components
  • Pre-mRNA-processing-splicing factor 8
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
KeywordsRNA BINDING PROTEIN / RecA domain / winged helix domain / Sec63 unit / Jab1/MPN domain / Pre-mRNA splicing / ATP binding / RNA binding / ubiquitin binding
Function / homology
Function and homology information


cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / RNA helicase activity / nuclear speck / 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 / Cytidine Deaminase, domain 2 / Winged Helix-turn-helix domain / Sec63 Brl 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 / Cytidine Deaminase, domain 2 / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Cytidine Deaminase; domain 2 / Sec63 domain / Sec63 Brl domain / C2 domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / C2 domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Arc Repressor Mutant, subunit A / 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 / Ribonuclease H-like superfamily / 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 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.598 Å
AuthorsWahl, M.C. / Wandersleben, T. / Santos, K.F.
CitationJournal: Science / Year: 2013
Title: Inhibition of RNA helicase Brr2 by the C-terminal tail of the spliceosomal protein Prp8.
Authors: Mozaffari-Jovin, S. / Wandersleben, T. / Santos, K.F. / Will, C.L. / Luhrmann, R. / Wahl, M.C.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 20, 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 / database_2 / pdbx_initial_refinement_model / 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
C: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,5255
Polymers230,6472
Non-polymers8793
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-38 kcal/mol
Surface area84710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.002, 240.002, 201.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Brr2 protein / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP- ...Brr2 protein / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 198785.797 Da / Num. of mol.: 1 / Fragment: helicase region (UNP residues 395-2129)
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
#2: Protein Pre-mRNA-processing-splicing factor 8 / Prp8 protein / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 31860.984 Da / Num. of mol.: 1 / Fragment: Jab1/MPN domain (UNP residues 2064-2335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF8, PRPC8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6P2Q9
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 6.3 Å3/Da / Density % sol: 80.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1 M HEPES-NaOH, pH 7.9, 0.2 M magnesium chloride, 12% ethanol, Silver Bullets Bio condition 91 (Hampton Research) as additive, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 19, 2012
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.598→50 Å / Num. all: 68276 / Num. obs: 68276 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 14.4
Reflection shellResolution: 3.598→3.8 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.725 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4F91 AND 2OG4

4f91

2og4


Resolution: 3.598→49.204 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 3412 5 %
Rwork0.1972 --
obs0.1991 68248 99.75 %
all-68276 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.598→49.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16031 0 55 0 16086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816452
X-RAY DIFFRACTIONf_angle_d1.21122319
X-RAY DIFFRACTIONf_dihedral_angle_d17.6666190
X-RAY DIFFRACTIONf_chiral_restr0.0862503
X-RAY DIFFRACTIONf_plane_restr0.0062854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.598-3.64930.36621370.32052605X-RAY DIFFRACTION97
3.6493-3.70380.33631390.28182640X-RAY DIFFRACTION100
3.7038-3.76170.33531400.26592670X-RAY DIFFRACTION100
3.7617-3.82330.28261410.24512668X-RAY DIFFRACTION100
3.8233-3.88920.24871400.24342661X-RAY DIFFRACTION100
3.8892-3.95990.28251410.23112681X-RAY DIFFRACTION100
3.9599-4.0360.26581420.21872692X-RAY DIFFRACTION100
4.036-4.11840.25631390.20882658X-RAY DIFFRACTION100
4.1184-4.20790.23351410.22674X-RAY DIFFRACTION100
4.2079-4.30570.21781410.1762671X-RAY DIFFRACTION100
4.3057-4.41330.20711420.17372702X-RAY DIFFRACTION100
4.4133-4.53260.191410.16032674X-RAY DIFFRACTION100
4.5326-4.66580.19551400.15772672X-RAY DIFFRACTION100
4.6658-4.81630.19791430.16252707X-RAY DIFFRACTION100
4.8163-4.98830.21011410.16052678X-RAY DIFFRACTION100
4.9883-5.18780.19831420.16642697X-RAY DIFFRACTION100
5.1878-5.42360.211430.17112716X-RAY DIFFRACTION100
5.4236-5.70920.21891430.18882716X-RAY DIFFRACTION100
5.7092-6.06630.24741430.20222719X-RAY DIFFRACTION100
6.0663-6.53370.27741430.21572726X-RAY DIFFRACTION100
6.5337-7.18940.24151440.20092739X-RAY DIFFRACTION100
7.1894-8.22550.19531470.17892774X-RAY DIFFRACTION100
8.2255-10.34740.17121460.15982791X-RAY DIFFRACTION100
10.3474-49.2090.28151530.22852905X-RAY DIFFRACTION99
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)
11.6338-0.61870.27340.2512-0.2150.64740.1665-1.0290.75630.242-0.2770.1255-0.2738-0.86890.0211.34940.25870.37562.4016-0.76851.8889-15.555172.427663.87
20.74630.04850.0814.79560.26122.4737-0.0418-1.01020.65350.51080.0928-0.93480.05830.1512-0.15581.23570.23450.01432.6494-1.25342.1213-0.061861.453357.9055
31.6841.56080.46821.5882-0.21922.9988-0.4832-0.57741.1205-0.59180.0046-0.0376-0.85390.19130.18951.61130.20060.55542.182-1.1912.6177-19.391984.686945.0715
40.97110.66331.0583.3019-0.61942.4533-0.3103-1.30220.29770.91530.63030.33690.37080.244-0.23221.31990.22730.29742.5591-0.64271.3745-17.032742.000656.2965
54.0678-1.81660.11214.8084-0.17054.41210.0869-0.71291.176-0.00810.110.1106-0.4271-0.619-0.18930.8128-0.00130.31031.4164-0.60841.5105-17.139252.785226.2281
64.57091.56370.69594.4377-1.79334.9578-0.09490.55740.9722-0.147-0.1469-0.0423-0.2258-0.17380.19641.3207-0.18240.63371.2721-0.40332.38897.339364.084211.0987
72.7056-0.5020.95315.88560.45983.87590.0188-0.83731.13390.13110.4441-0.7884-0.38270.3664-0.37620.631-0.10650.22321.2027-0.51811.21389.383738.360522.0772
85.76430.96750.48724.21530.37723.1587-0.1939-1.51770.00710.98930.5309-0.57560.47670.5312-0.34541.13040.1185-0.22781.6805-0.29990.877629.53524.206540.6385
90.882-0.09240.3514.19240.81613.4087-0.1403-0.91920.32891.04240.3085-0.4134-0.0406-0.3742-0.16771.31140.24420.03772.382-0.50481.059313.288827.0253.0611
104.94421.06761.11772.9778-0.84062.05180.05530.18950.45870.0880.4052-0.8475-0.27770.7683-0.44060.8479-0.15290.08981.3656-0.71651.248937.120918.885417.7438
112.5552-0.29970.37292.0543-0.63952.68380.4597-0.41260.46460.34330.17740.3343-1.08310.3814-0.47031.4812-0.2510.20721.9204-1.09382.169344.869240.128439.816
122.1929-0.14120.39431.7309-2.42123.3856-0.6941-1.10860.63640.77820.0196-0.1928-0.74090.20770.42012.0499-0.4352-0.07142.5126-0.58781.620161.379237.87964.8754
133.4933-0.8327-0.42710.7912-0.15612.26620.494-0.5661-0.19960.63920.0351-0.4160.32410.5707-0.491.5958-0.528-0.23452.1428-0.92742.0169.588328.761939.7959
143.0493-0.24790.84993.91091.55336.31260.2025-0.2150.8828-0.456-0.0723-0.0266-0.6933-0.359-0.16120.7392-0.10810.3170.6718-0.0320.9858-9.96737.6-1.3082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 404:486)
2X-RAY DIFFRACTION2chain 'B' and (resseq 487:683)
3X-RAY DIFFRACTION3chain 'B' and (resseq 684:888)
4X-RAY DIFFRACTION4chain 'B' and (resseq 889:993)
5X-RAY DIFFRACTION5chain 'B' and (resseq 994:1125)
6X-RAY DIFFRACTION6chain 'B' and (resseq 1126:1181)
7X-RAY DIFFRACTION7chain 'B' and (resseq 1182:1294)
8X-RAY DIFFRACTION8chain 'B' and (resseq 1295:1521)
9X-RAY DIFFRACTION9chain 'B' and (resseq 1522:1724)
10X-RAY DIFFRACTION10chain 'B' and (resseq 1725:1824)
11X-RAY DIFFRACTION11chain 'B' and (resseq 1825:1957)
12X-RAY DIFFRACTION12chain 'B' and (resseq 1958:2014)
13X-RAY DIFFRACTION13chain 'B' and (resseq 2015:2125)
14X-RAY DIFFRACTION14chain 'C' and (resseq 2067:2335)

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