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- PDB-4ru2: Crystal structure of a RNA-binding protein 39 (RBM39) in complex ... -

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Basic information

Entry
Database: PDB / ID: 4ru2
TitleCrystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution
Components
  • RNA-binding protein 39 (RBM39)
  • 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 / 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 / RND3 GTPase cycle / Protein hydroxylation / RS domain binding / RAC3 GTPase cycle ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / 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 / RND3 GTPase cycle / Protein hydroxylation / RS domain binding / RAC3 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RND2 GTPase cycle / U2AF complex / RND1 GTPase cycle / RAC1 GTPase cycle / pre-mRNA 3'-splice site binding / RHOG GTPase cycle / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / Prp19 complex / U2-type prespliceosome / 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 / transcription coactivator activity / nuclear speck / regulation of transcription by RNA polymerase II / 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: To be published
Title: Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: 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

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Assembly

Deposited unit
A: RNA-binding protein 39 (RBM39)
B: Splicing factor U2AF 65 kDa subunit
C: RNA-binding protein 39 (RBM39)
D: Splicing factor U2AF 65 kDa subunit
E: RNA-binding protein 39 (RBM39)
F: Splicing factor U2AF 65 kDa subunit
G: RNA-binding protein 39 (RBM39)
H: Splicing factor U2AF 65 kDa subunit
I: RNA-binding protein 39 (RBM39)
J: Splicing factor U2AF 65 kDa subunit
K: RNA-binding protein 39 (RBM39)
L: Splicing factor U2AF 65 kDa subunit
M: RNA-binding protein 39 (RBM39)
N: Splicing factor U2AF 65 kDa subunit
O: RNA-binding protein 39 (RBM39)
P: Splicing factor U2AF 65 kDa subunit
Q: RNA-binding protein 39 (RBM39)
R: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)144,55318
Polymers144,55318
Non-polymers00
Water9,674537
1
A: RNA-binding protein 39 (RBM39)
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 area6730 Å2
MethodPISA
2
C: RNA-binding protein 39 (RBM39)
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 area980 Å2
ΔGint-4 kcal/mol
Surface area7050 Å2
MethodPISA
3
E: RNA-binding protein 39 (RBM39)
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-5 kcal/mol
Surface area6550 Å2
MethodPISA
4
G: RNA-binding protein 39 (RBM39)
H: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)16,0612
Polymers16,0612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area7010 Å2
MethodPISA
5
I: RNA-binding protein 39 (RBM39)
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-5 kcal/mol
Surface area6910 Å2
MethodPISA
6
K: RNA-binding protein 39 (RBM39)
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-5 kcal/mol
Surface area6750 Å2
MethodPISA
7
M: RNA-binding protein 39 (RBM39)
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-5 kcal/mol
Surface area7020 Å2
MethodPISA
8
O: RNA-binding protein 39 (RBM39)
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 area6760 Å2
MethodPISA
9
Q: RNA-binding protein 39 (RBM39)
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 area970 Å2
ΔGint-4 kcal/mol
Surface area6620 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

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Components

#1: Protein
RNA-binding protein 39 (RBM39) / 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: CAPER, RBM39, RNPC2, WS20613E / Plasmid: SpeedET / 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, WT4514D / Plasmid: pGEX4T / 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.: 537 / Source method: isolated from a natural source / Formula: H2O
Sequence 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 P26369 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, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1
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
ReflectionResolution: 2.2→39.432 Å / Num. obs: 72455 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obs% possible all
2.2-2.260.7170.832184365374526998
2.26-2.320.7170.8632.3201275254524299.8
2.32-2.390.7850.7482.8195295080507499.9
2.39-2.460.8190.6383.3190234934492599.8
2.46-2.540.870.5094186424827482099.9
2.54-2.630.9120.4134.7179424639463199.8
2.63-2.730.9330.3495.5171914465446199.9
2.73-2.840.9580.2686.7166794305430199.9
2.84-2.970.9730.2038.2159194119411699.9
2.97-3.110.9880.14310.4153323977397599.9
3.11-3.280.990.10812.9142623743373999.9
3.28-3.480.9940.08614.7134083564355599.7
3.48-3.720.9950.06717.6123793301329399.8
3.72-4.010.9950.05819.4116723105310399.9
4.01-4.40.9980.04821.4108962880287799.9
4.4-4.920.9980.04422.3973025652564100
4.92-5.680.9980.04721.386472281227999.9
5.68-6.950.9980.04520.172981919191899.9
6.95-9.830.9990.0362357361494149299.9
9.830.9970.03626.6300680779398.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S6E

3s6e


Resolution: 2.2→39.432 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
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 BUSTER'S LSSR RESTRAINT REPRESENTATION ...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 BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 3.DURING REFINEMENT, SIDECHAIN TYR468 ON THE A,E,G,I,K,M,O AND Q SUBUNITS MOVED OUT OF DENSITY. TO IMPROVE THE FIT OF THESE TYR468 SIDECHAINS TO THEIR ELECTRON DENSITIES SOME VAN DER WAALS CONTACT RESTRAINTS BETWEEN THESE TYR468 RESIDUES AND SOME NEARBY RESIDUES AND WATER MOLECULES WERE EXCLUDED FROM THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3644 5.04 %RANDOM
Rwork0.174 ---
obs0.176 72264 99.7 %-
Displacement parametersBiso max: 148.55 Å2 / Biso mean: 43.298 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.946 Å20 Å20 Å2
2---3.946 Å20 Å2
3---7.892 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8553 0 0 537 9090
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 258 4.92 %
Rwork0.212 4985 -
all0.213 5243 -
obs--99.7 %
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)
11.9925-0.44730.13941.6708-0.46924.21130.0771-0.28140.0327-0.0572-0.03260.056-0.0246-0.0239-0.0445-0.1035-0.0299-0.00940.01030.0223-0.099487.991466.9005-21.3721
22.3804-0.50980.34432.9478-0.74293.6734-0.15820.0004-0.0154-0.02010.2338-0.02210.0225-0.0044-0.0756-0.0616-0.0242-0.0448-0.05290.0074-0.123103.474342.3733-15.0956
33.14710.14740.95572.9730.51655.76030.15180.01450.30230.3221-0.20790.1692-0.29870.04930.0562-0.0957-0.08750.05-0.1322-0.0243-0.0915120.995473.9519-12.5529
42.99980.3596-0.84862.3261-0.44624.00440.09970.134800.1583-0.0574-0.0506-0.25350.1128-0.0423-0.0393-0.06680.0173-0.079-0.0387-0.11877.641772.93074.8815
52.7869-0.3315-0.54021.81270.11584.04920.14470.00670.0678-0.1911-0.08690.0368-0.243-0.0237-0.0578-0.02760.0710.0259-0.07920.0097-0.110448.66874.045511.0049
62.7848-0.19210.08283.7453-0.01575.7146-0.18090.0626-0.1316-0.14430.23030.29030.25-0.2992-0.0495-0.0819-0.0536-0.0404-0.17620.0219-0.068359.719741.83452.1327
71.73880.40710.00112.52080.55534.3775-0.1251-0.0405-0.06750.10340.1743-0.03970.08110.0962-0.0491-0.0190.0362-0.0324-0.0934-0.0088-0.105687.667978.352831.2814
82.64670.52380.83723.1660.61634.98790.07040.21770.07560.1805-0.03030.01690.02840.1758-0.0401-0.0949-0.02340.0238-0.047-0.0293-0.1279102.1054103.446337.3748
93.7178-0.4774-0.35332.72610.04295.80810.1094-0.4093-0.2061-0.0122-0.06820.16490.1277-0.4549-0.0412-0.20090.0049-0.0066-0.01880.0528-0.094366.1282104.444640.3932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|420-530 B|89-97}A420
2X-RAY DIFFRACTION1{A|420-530 B|89-97}B89
3X-RAY DIFFRACTION2{C|419-530 D|88-98}C419
4X-RAY DIFFRACTION2{C|419-530 D|88-98}D88
5X-RAY DIFFRACTION3{E|418-529 F|89-98}E418
6X-RAY DIFFRACTION3{E|418-529 F|89-98}F89
7X-RAY DIFFRACTION4{G|419-530 H|88-98}G419
8X-RAY DIFFRACTION4{G|419-530 H|88-98}H88
9X-RAY DIFFRACTION5{I|420-530 J|88-98}I420
10X-RAY DIFFRACTION5{I|420-530 J|88-98}J88
11X-RAY DIFFRACTION6{K|0-529 L|88-98}K0
12X-RAY DIFFRACTION6{K|0-529 L|88-98}L88
13X-RAY DIFFRACTION7{M|420-530 N|88-98}M420
14X-RAY DIFFRACTION7{M|420-530 N|88-98}N88
15X-RAY DIFFRACTION8{O|420-529 P|88-97}O420
16X-RAY DIFFRACTION8{O|420-529 P|88-97}P88
17X-RAY DIFFRACTION9{Q|418-529 R|89-98}Q418
18X-RAY DIFFRACTION9{Q|418-529 R|89-98}R89

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