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- PDB-7pjh: Crystal structure of the human spliceosomal maturation factor AAR... -

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Basic information

Entry
Database: PDB / ID: 7pjh
TitleCrystal structure of the human spliceosomal maturation factor AAR2 bound to the RNAse H domain of PRPF8
Components
  • Pre-mRNA-processing-splicing factor 8
  • Protein AAR2 homolog
KeywordsSPLICING / Spliceosomal maturation / pre-mRNA splicing / human AAR2 / human PRPF8
Function / homology
Function and homology information


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 ...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 / mRNA splicing, via spliceosome / mRNA processing / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / nuclear speck / RNA binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal 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. / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-processing-splicing factor 8 / Protein AAR2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPreussner, M. / Santos, K. / Heroven, A.C. / Alles, J. / Heyd, F. / Wahl, M.C. / Weber, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR186/A15 Germany
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8.
Authors: Preussner, M. / Santos, K.F. / Alles, J. / Heroven, C. / Heyd, F. / Wahl, M.C. / Weber, G.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta crystallographica. Section D, Structural biology
Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionAug 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AAR2 homolog
B: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)75,3912
Polymers75,3912
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-11 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.280, 57.260, 111.230
Angle α, β, γ (deg.)90.000, 112.740, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Protein AAR2 homolog / AAR2 splicing factor homolog


Mass: 45680.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAR2, C20orf4, CGI-23, PRO0225 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y312
#2: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 29710.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF8, PRPC8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6P2Q9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.0, 10% PEG 6000, 5%(v/v) 2-methyl-2,4- pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2395 Å / Relative weight: 1
ReflectionResolution: 2.35→48.233 Å / Num. obs: 34687 / % possible obs: 97.6 % / Redundancy: 3.79 % / Biso Wilson estimate: 55.39 Å2 / CC1/2: 0.99 / Net I/σ(I): 1.7
Reflection shellResolution: 2.35→2.41 Å / Num. unique obs: 2502 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E9L

3e9l


Resolution: 2.35→48.21 Å / SU ML: 0.3483 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 33.0134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1721 4.96 %
Rwork0.1888 32957 -
obs0.1912 34678 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.42 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 0 147 4765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00884761
X-RAY DIFFRACTIONf_angle_d0.98966467
X-RAY DIFFRACTIONf_chiral_restr0.0609732
X-RAY DIFFRACTIONf_plane_restr0.0098820
X-RAY DIFFRACTIONf_dihedral_angle_d15.91961767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.420.41831300.34742667X-RAY DIFFRACTION95.69
2.42-2.50.3271520.31332729X-RAY DIFFRACTION97.5
2.5-2.590.38451380.30062696X-RAY DIFFRACTION97.09
2.59-2.690.35961490.29322742X-RAY DIFFRACTION98
2.69-2.810.31091420.24382685X-RAY DIFFRACTION97.18
2.81-2.960.30411350.21362746X-RAY DIFFRACTION97.63
2.96-3.150.28241430.2162736X-RAY DIFFRACTION97.56
3.15-3.390.28021450.21042737X-RAY DIFFRACTION97.66
3.39-3.730.19731400.17382761X-RAY DIFFRACTION98.31
3.73-4.270.19571490.15722759X-RAY DIFFRACTION98.38
4.27-5.380.19041470.15252819X-RAY DIFFRACTION99
5.38-48.210.20221510.16392880X-RAY DIFFRACTION98.7
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)
14.591808156832.34706194231.20056863443.74813917944-2.249898057637.31342793447-0.172123769297-0.510387816679-0.2453521764990.08803873577010.170982541846-0.2251164087560.5620062638490.3605215565380.07513502148760.4577104978270.09851405073390.006498552846760.5805203339180.01916059462620.41180432256335.926546199439.655308764655.4832260514
23.63229553742-1.317492279320.8032881471615.08381382964-0.7868415592814.95171860487-0.196238275725-0.6562183082030.2875040896620.452909856571-0.1108641912790.206347510661-0.4208085743790.02243000660560.2945945967350.534222672080.0609297549380.03171542456360.676091150547-0.0181870663320.40475144661235.415682975348.018798273156.9532315025
34.11627580677-1.76298298983.439410137790.731393871745-1.596339741095.43907783246-0.278014590154-0.1480169163760.3906813868130.08027908935460.121634192221-0.161375972712-0.32248199411-0.06442069928940.1158247334290.453967933330.00310730074529-0.005719585695410.3925091360360.03413632736750.52951974649622.095542699553.738739120733.7644042539
45.53469793696-0.7914828746413.120487979724.81587140277-0.6627126427933.610036606850.4349157813550.319407736786-0.797530038827-0.319923567778-0.07821147045860.4218762592980.8899857367990.0874540630485-0.4170365482350.5848412958760.0596019136241-0.07322264421680.428336343804-0.03615401669910.60999230622916.555259503641.220870683124.3570464636
55.94869357272-3.719498662752.193723265354.86362407385-4.014492499933.558476555550.3748118769790.0550281787095-1.275916635510.429487759930.2330550688010.195836303552-0.03485612738560.0890076815445-0.7296985449250.613868178551-0.0928968505092-0.04712474454470.611299906241-0.0333247570710.753400862142-3.3561659148940.912631081517.9920414415
62.75770192787-0.363924633036-0.7392438440584.398449096512.177991813554.641219195630.119680259642-0.398856696656-0.1423222355330.0775547363195-0.3353217030830.318539019643-0.0759225441249-0.5294172932850.2949798381620.358977833599-0.0326167543656-0.05159895633110.503676231292-0.03134852834770.508605492926-12.172845630354.677924798520.3976379146
73.250340685860.0807535366608-0.8189528607252.90166732241.875569653292.984252557610.146664247378-0.1035674511940.00304386899958-0.0267880723063-0.3457841106260.0923301458555-0.240392019261-0.1667539912390.2000808514520.5073052401180.0344475002025-0.01863368832590.5240191867640.02334187305750.390056204708-7.3273714803260.301497309117.7465524115
86.19337027941-2.20125212801-3.159522020053.188387064850.9823122742945.767629334140.07390102638020.387482244405-0.180087137999-0.493444062179-0.4997652865480.827538259641-0.594614339507-1.211946332150.4598492763530.5091793401250.100018167558-0.1548091162260.698603509949-0.1411393787110.664290755875-21.773516739559.483798240510.6396253855
96.20867728586-1.486028957870.6632423391683.85410796209-0.7050643536453.591668600380.156360684131-0.251661885976-0.852473431449-0.358219813445-0.1906557018131.38509516510.366750228733-0.956002256276-0.02988125195960.56116071065-0.0613749507849-0.03903123199131.04081285616-0.2000786509781.09491692738-32.444105218551.355994522117.6153833583
100.5317370125020.0504980386467-0.2279876199291.89482464739-1.39581444411.13015514527-0.246584223095-0.420416930032-0.1522492387980.4277794833711.06206601777-0.2167762577050.1854055624980.0772962472393-0.719277760710.892578993401-0.3997621500750.1636229594621.503963361890.01320270058341.3139600427-28.58684130144.881161859734.0261854834
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 53 )AA10 - 531 - 44
22chain 'A' and (resid 54 through 124 )AA54 - 12445 - 115
33chain 'A' and (resid 125 through 282 )AA125 - 282116 - 230
44chain 'A' and (resid 283 through 359 )AA283 - 359231 - 298
55chain 'A' and (resid 360 through 378 )AA360 - 378299 - 317
66chain 'B' and (resid 1758 through 1797 )BB1758 - 17971 - 40
77chain 'B' and (resid 1798 through 1892 )BB1798 - 189241 - 135
88chain 'B' and (resid 1893 through 1928 )BB1893 - 1928136 - 171
99chain 'B' and (resid 1929 through 1995 )BB1929 - 1995172 - 238
1010chain 'B' and (resid 1996 through 2014 )BB1996 - 2014239 - 257

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