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- PDB-1syx: The crystal structure of a binary U5 snRNP complex -

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Basic information

Entry
Database: PDB / ID: 1syx
TitleThe crystal structure of a binary U5 snRNP complex
Components
  • CD2 antigen cytoplasmic tail-binding protein 2
  • Spliceosomal U5 snRNP-specific 15 kDa protein
KeywordsTRANSLATION/IMMUNE SYSTEM / GYF-domain / thioredoxin-like / spliceosomal proteins / TRANSLATION-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNP / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex ...RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNP / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / nuclear speck / cell division / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
GYF domain / CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 ...GYF domain / CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / Dna Ligase; domain 1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CD2 antigen cytoplasmic tail-binding protein 2 / Thioredoxin-like protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.345 Å
AuthorsNielsen, T.K. / Liu, S. / Luhrmann, R. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis for the bifunctionality of the U5 snRNP 52K protein (CD2BP2).
Authors: Nielsen, T.K. / Liu, S. / Luhrmann, R. / Ficner, R.
History
DepositionApr 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spliceosomal U5 snRNP-specific 15 kDa protein
C: Spliceosomal U5 snRNP-specific 15 kDa protein
E: Spliceosomal U5 snRNP-specific 15 kDa protein
B: CD2 antigen cytoplasmic tail-binding protein 2
D: CD2 antigen cytoplasmic tail-binding protein 2
F: CD2 antigen cytoplasmic tail-binding protein 2


Theoretical massNumber of molelcules
Total (without water)80,0496
Polymers80,0496
Non-polymers00
Water3,459192
1
A: Spliceosomal U5 snRNP-specific 15 kDa protein
B: CD2 antigen cytoplasmic tail-binding protein 2


Theoretical massNumber of molelcules
Total (without water)26,6832
Polymers26,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spliceosomal U5 snRNP-specific 15 kDa protein
D: CD2 antigen cytoplasmic tail-binding protein 2


Theoretical massNumber of molelcules
Total (without water)26,6832
Polymers26,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Spliceosomal U5 snRNP-specific 15 kDa protein
F: CD2 antigen cytoplasmic tail-binding protein 2


Theoretical massNumber of molelcules
Total (without water)26,6832
Polymers26,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.726, 75.913, 77.027
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 5

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1TYRTYRTYRTYRAA3 - 1363 - 136
2VALVALTHRTHRBD26 - 8626 - 86
3TYRTYRTYRTYRCB3 - 1363 - 136
4VALVALTHRTHRDE26 - 8626 - 86
5TYRTYRTYRTYREC3 - 1363 - 136
6VALVALTHRTHRFF26 - 8626 - 86

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Components

#1: Protein Spliceosomal U5 snRNP-specific 15 kDa protein / U5-15kD / DIM1 protein homolog / Thioredoxin-like U5 snRNP protein U5-15kD / thioredoxin-like 4


Mass: 16807.346 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U5-15KD / Plasmid: PXC35-15K / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P83876
#2: Protein CD2 antigen cytoplasmic tail-binding protein 2 / CD2BP2 / CD2 cytoplasmic domain binding protein / CD2 tail binding protein


Mass: 9875.679 Da / Num. of mol.: 3 / Fragment: 86 amino acid C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD2BP2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: O95400
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONEMBL/DESY, HAMBURG X1320.8
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEMar 1, 2003mirrors
MARRESEARCH2CCDAug 24, 2003mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Triangular monochromator, bent mirror
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.81
ReflectionResolution: 2.345→50 Å / Num. all: 30397 / Num. obs: 30397 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.031
Reflection shellResolution: 2.345→2.39 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1535 / Rsym value: 0.248 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGV and 1GYF

1qgv

1gyf


Resolution: 2.345→49.39 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.619 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26249 1486 4.9 %RANDOM
Rwork0.21578 ---
all0.217 30297 --
obs0.21806 28709 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.592 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.345→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 0 192 5082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224967
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9336727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155585
X-RAY DIFFRACTIONr_chiral_restr0.0740.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023861
X-RAY DIFFRACTIONr_gen_planes_other0.040.025
X-RAY DIFFRACTIONr_nbd_refined0.1990.22126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.213
X-RAY DIFFRACTIONr_mcbond_it0.4051.52941
X-RAY DIFFRACTIONr_mcangle_it0.77424757
X-RAY DIFFRACTIONr_scbond_it1.17732026
X-RAY DIFFRACTIONr_scangle_it1.8784.51970
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A16medium positional2.250.5
3C16medium positional2.20.5
5E16medium positional2.240.5
1A14loose positional2.945
3C14loose positional2.765
5E14loose positional2.955
1A16medium thermal1.182
3C16medium thermal0.522
5E16medium thermal0.732
1A14loose thermal1.7710
3C14loose thermal1.0110
5E14loose thermal0.7810
LS refinement shellResolution: 2.345→2.406 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.308 105
Rwork0.278 2119
obs-2119
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)
12.36540.3544-1.74412.6961-0.45173.3077-0.06830.32680.0044-0.13420.0966-0.05130.0127-0.0294-0.02830.0714-0.0339-0.00080.060.0130.05946.2673-0.087619.699
26.4621-0.3329-2.41643.8292-1.99975.82440.02270.05170.20630.06180.089-0.1525-0.2330.0248-0.11180.1238-0.08810.01460.29830.04090.094621.64576.132-1.3262
34.69690.80771.4583.31671.17153.31380.08650.1532-0.5326-0.0290.1495-0.10190.33810.0521-0.2360.1519-0.02630.00340.03020.00760.132864.95669.416423.0662
47.06810.29824.38182.18621.21639.8386-0.1386-0.26750.41370.0425-0.10140.0645-0.2192-0.41580.240.162-0.1084-0.01920.28110.02390.236340.21227.472812.7165
54.9075-0.62942.24461.8001-0.37453.7206-0.15980.27750.5749-0.0106-0.1085-0.0162-0.3936-0.10250.26830.17430.02910.00810.01340.0420.1929115.228717.452234.385
66.9948-0.58171.42654.72251.83135.0333-0.06860.25790.061-0.20050.0519-0.0737-0.19560.00260.01670.13010.0710.05850.23210.00410.085796.99938.770517.0634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1363 - 136
2X-RAY DIFFRACTION2BD25 - 8625 - 86
3X-RAY DIFFRACTION3CB3 - 1363 - 136
4X-RAY DIFFRACTION4DE25 - 8625 - 86
5X-RAY DIFFRACTION5EC3 - 1363 - 136
6X-RAY DIFFRACTION6FF25 - 8625 - 86

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