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- PDB-5cxt: Crystal structure of a RNA-binding protein 39 (RBM39) in complex ... -

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Basic information

Entry
Database: PDB / ID: 5cxt
TitleCrystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution
Components
  • RNA-binding protein 39
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN / RBM39linker (PF15519) / RNA recognition motif (PF13893) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Protein hydroxylation / RAC3 GTPase cycle / RS domain binding ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Protein hydroxylation / RAC3 GTPase cycle / RS domain binding / RAC2 GTPase cycle / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle / U2AF complex / RND2 GTPase cycle / RND1 GTPase cycle / RHOG GTPase cycle / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Prp19 complex / U1 snRNP binding / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / commitment complex / U2-type prespliceosome / spliceosomal complex assembly / negative regulation of mRNA splicing, via spliceosome / centriolar satellite / negative regulation of protein ubiquitination / RNA splicing / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / enzyme binding / protein-containing complex / RNA binding / nucleus
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / U2 snRNP auxilliary factor, large subunit, splicing factor / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / U2 snRNP auxilliary factor, large subunit, splicing factor / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Splicing factor U2AF 65 kDa subunit / RNA-binding protein 39
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.
Authors: Stepanyuk, G.A. / Serrano, P. / Peralta, E. / Farr, C.L. / Axelrod, H.L. / Geralt, M. / Das, D. / Chiu, H.J. / Jaroszewski, L. / Deacon, A.M. / Lesley, S.A. / Elsliger, M.A. / Godzik, A. / ...Authors: Stepanyuk, G.A. / Serrano, P. / Peralta, E. / Farr, C.L. / Axelrod, H.L. / Geralt, M. / Das, D. / Chiu, H.J. / Jaroszewski, L. / Deacon, A.M. / Lesley, S.A. / Elsliger, M.A. / Godzik, A. / Wilson, I.A. / Wuthrich, K. / Salomon, D.R. / Williamson, J.R.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Derived calculations
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Sep 27, 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_oper_list
Item: _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: RNA-binding protein 39
B: Splicing factor U2AF 65 kDa subunit
C: RNA-binding protein 39
D: Splicing factor U2AF 65 kDa subunit
E: RNA-binding protein 39
F: Splicing factor U2AF 65 kDa subunit
G: RNA-binding protein 39
H: Splicing factor U2AF 65 kDa subunit
I: RNA-binding protein 39
J: Splicing factor U2AF 65 kDa subunit
K: RNA-binding protein 39
L: Splicing factor U2AF 65 kDa subunit
M: RNA-binding protein 39
N: Splicing factor U2AF 65 kDa subunit
O: RNA-binding protein 39
P: Splicing factor U2AF 65 kDa subunit
Q: RNA-binding protein 39
R: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)144,55318
Polymers144,55318
Non-polymers00
Water9,332518
1
A: RNA-binding protein 39
B: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area6710 Å2
MethodPISA
2
C: RNA-binding protein 39
D: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-4 kcal/mol
Surface area7040 Å2
MethodPISA
3
E: RNA-binding protein 39
F: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area6560 Å2
MethodPISA
4
G: RNA-binding protein 39
H: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-5 kcal/mol
Surface area6990 Å2
MethodPISA
5
I: RNA-binding protein 39
J: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area6900 Å2
MethodPISA
6
K: RNA-binding protein 39
L: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area6780 Å2
MethodPISA
7
M: RNA-binding protein 39
N: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area7040 Å2
MethodPISA
8
O: RNA-binding protein 39
P: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area6770 Å2
MethodPISA
9
Q: RNA-binding protein 39
R: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.283, 127.283, 78.864
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Detailsauthors state the following: The biological assembly predicted by PISA is irrelevant. The Biological Assembly is not really applicable in this case, since we are these are not full length proteins. This is a complex of a domain of one protein bound to a peptide derived from another protein.

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Components

#1: Protein
RNA-binding protein 39 / Coactivator of activating protein 1 and estrogen receptors / Coactivator of AP-1 and ERs / RNA- ...Coactivator of activating protein 1 and estrogen receptors / Coactivator of AP-1 and ERs / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Transcription coactivator CAPER


Mass: 12622.324 Da / Num. of mol.: 9 / Fragment: UNP residues 418-530 / Mutation: N468Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbm39, Caper, Rnpc2 / Plasmid: pGEX4T / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8VH51
#2: Protein/peptide
Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / U2 snRNP auxiliary factor large subunit


Mass: 3439.078 Da / Num. of mol.: 9 / Fragment: UNP residues 85-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: U2af2, U2af65 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: P26369
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CRYSTAL STRUCTURE CONSISTS OF TWO DIFFERENT CONSTRUCTS. BOTH CONSTRUCTS WERE EXPRESSED WITH AN ...THE CRYSTAL STRUCTURE CONSISTS OF TWO DIFFERENT CONSTRUCTS. BOTH CONSTRUCTS WERE EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAGS WERE REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 85-112 OF THE TARGET SEQUENCE OF UNIPROTKB ID P62369 AND RESIDUES 418-530 OF THE TARGET SEQUENCE OF UNIPROTKB ID Q8VH51.THE SEQUENCE NUMBERING OF UNIPROTKB P26369 IS BASED ON THE ISOFORM THAT MATCHES THE CANONICAL HUMAN ISOFORM UNIPROT ID P26368, AND THE SEQUENCE NUMBERING OF UNIPROT Q8VH51 IS BASED ON ISOFORM 1 OF THIS TARGET. IN THE Q8VH51 CONSTRUCT ASN 468 HAS BEEN MUTATED TO A TYR.

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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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M potassium chloride, 15.0% polyethylene glycol monomethyl ether 5000, 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2013
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.806
11-K, -H, -L20.194
ReflectionResolution: 2.2→39.432 Å / Num. obs: 72455 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.809 % / Biso Wilson estimate: 34.1 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.135 / Net I/σ(I): 9.71 / Num. measured all: 275854
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.2-2.260.7170.83218436537452690.981198
2.26-2.320.7170.8632.320127525452421.00799.8
2.32-2.390.7850.7482.819529508050740.87199.9
2.39-2.460.8190.6383.319023493449250.74399.8
2.46-2.540.870.509418642482748200.59299.9
2.54-2.630.9120.4134.717942463946310.4899.8
2.63-2.730.9330.3495.517191446544610.40699.9
2.73-2.840.9580.2686.716679430543010.31299.9
2.84-2.970.9730.2038.215919411941160.23699.9
2.97-3.110.9880.14310.415332397739750.16699.9
3.11-3.280.990.10812.914262374337390.12699.9
3.28-3.480.9940.08614.713408356435550.199.7
3.48-3.720.9950.06717.612379330132930.07999.8
3.72-4.010.9950.05819.411672310531030.06899.9
4.01-4.40.9980.04821.410896288028770.05699.9
4.4-4.920.9980.04422.39730256525640.052100
4.92-5.680.9980.04721.38647228122790.05599.9
5.68-6.950.9980.04520.17298191919180.05299.9
6.95-9.830.9990.036235736149414920.04299.9
9.83-39.4320.9970.03626.630068077930.04198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0123refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S6E

3s6e


Resolution: 2.2→39.432 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.573 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2.NCS RESTRAINTS WERE APPLIED USING LOCAL RESTRAINT REPRESENTATION. 3. ...Details: 1.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2.NCS RESTRAINTS WERE APPLIED USING LOCAL RESTRAINT REPRESENTATION. 3. DURING REFINEMENT, SIDECHAIN TYR468 ON THE A,E,G,I,K,M,O AND Q SUBUNITS MOVED OUT OF DENSITY. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 3629 5 %RANDOM
Rwork0.1744 68634 --
obs0.1751 72263 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.02 Å2 / Biso mean: 39.3644 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.73 Å20 Å20 Å2
2--8.73 Å20 Å2
3----17.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8553 0 0 518 9071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228883
X-RAY DIFFRACTIONr_bond_other_d0.010.028231
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9412166
X-RAY DIFFRACTIONr_angle_other_deg1.493318966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.251110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9224.468385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.274151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3571530
X-RAY DIFFRACTIONr_chiral_restr0.1010.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110110
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022009
X-RAY DIFFRACTIONr_mcbond_it2.2823.1274407
X-RAY DIFFRACTIONr_mcbond_other2.283.1264406
X-RAY DIFFRACTIONr_mcangle_it3.7134.665486
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 253 -
Rwork0.244 4955 -
all-5208 -
obs--98.3 %
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)
10.7862-0.36030.24540.56360.0221.41270.0575-0.1136-0.0135-0.04520.00290.042-0.0202-0.0434-0.06040.0188-0.00130.00260.07450.02010.017488.261166.8977-21.3336
20.8714-0.3273-0.12361.2187-0.47040.9395-0.07010.0009-0.00630.00910.1264-0.01960.0187-0.0197-0.05630.0681-0.011-0.02720.0312-0.00040.0202103.545442.5843-15.0219
31.11280.18190.3140.7683-0.17811.82450.0710.03270.09830.1684-0.09060.0885-0.10010.05250.01960.055-0.03330.0370.0284-0.02290.0341120.830573.7666-12.6205
41.17640.1909-0.37650.6687-0.22921.03710.06360.0809-0.07140.0802-0.0326-0.0011-0.03440.0396-0.0310.0495-0.01150.02070.0417-0.02040.022977.501772.7484.8856
51.1584-0.1066-0.08130.44240.19051.11840.0707-0.0378-0.0162-0.1064-0.01220.0139-0.0444-0.0187-0.05840.05730.01530.02140.0370.00990.026648.747673.834611.0199
60.7154-0.1856-0.29831.6611-0.18842.1874-0.10510.0297-0.0309-0.07250.11730.12130.107-0.0785-0.01220.0434-0.0195-0.03620.01780.01150.074559.756642.05542.1855
70.44690.1336-0.23430.97550.37441.1876-0.0657-0.026-0.00540.01460.08690.0235-0.00780.0322-0.02120.05710.0244-0.02350.0453-0.00780.020487.586278.495731.2055
80.93990.36440.47361.03460.10351.31750.05030.09560.04330.0654-0.02970.05330.05640.0217-0.02060.02310.00340.00960.0642-0.02010.0196101.8445103.347837.4232
91.2956-0.31620.17460.8450.16152.17340.0585-0.1867-0.1078-0.052-0.06020.01710.0302-0.15770.00170.0052-0.0023-0.00260.0780.03570.031166.3314104.374240.3836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A420 - 530
2X-RAY DIFFRACTION1B89 - 97
3X-RAY DIFFRACTION2C419 - 530
4X-RAY DIFFRACTION2D88 - 98
5X-RAY DIFFRACTION3E418 - 529
6X-RAY DIFFRACTION3F88 - 98
7X-RAY DIFFRACTION4G419 - 530
8X-RAY DIFFRACTION4H88 - 98
9X-RAY DIFFRACTION5I420 - 530
10X-RAY DIFFRACTION5J88 - 98
11X-RAY DIFFRACTION6K0 - 529
12X-RAY DIFFRACTION6L88 - 98
13X-RAY DIFFRACTION7M420 - 530
14X-RAY DIFFRACTION7N88 - 98
15X-RAY DIFFRACTION8O420 - 529
16X-RAY DIFFRACTION8P88 - 97
17X-RAY DIFFRACTION9Q418 - 529
18X-RAY DIFFRACTION9R89 - 98

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