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- PDB-5f5v: Crystal structure of the Snu23-Prp38-MFAP1(217-296) complex of Ch... -

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Basic information

Entry
Database: PDB / ID: 5f5v
TitleCrystal structure of the Snu23-Prp38-MFAP1(217-296) complex of Chaetomium thermophilum
Components
  • Prp38
  • Putative uncharacterized protein
  • Zinc finger domain-containing protein
KeywordsSPLICING / B-specific protein / heterotrimer / pre-mRNA splicing / SAH / transcription
Function / homology
Function and homology information


U2-type spliceosomal complex / precatalytic spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA binding / zinc ion binding
Similarity search - Function
Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger ...Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Pre-mRNA-splicing factor 38 / Zinc finger domain-containing protein / Micro-fibrillar-associated protein 1 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsUlrich, A.K.C. / Seeger, M. / Bartlick, N. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWA1126/7-1 Germany
CitationJournal: Structure / Year: 2016
Title: Scaffolding in the Spliceosome via Single alpha Helices.
Authors: Ulrich, A.K.C. / Seeger, M. / Schutze, T. / Bartlick, N. / Wahl, M.C.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: 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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prp38
B: Putative uncharacterized protein
C: Zinc finger domain-containing protein
D: Prp38
E: Putative uncharacterized protein
F: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)79,8936
Polymers79,8936
Non-polymers00
Water00
1
A: Prp38
B: Putative uncharacterized protein
C: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Prp38
E: Putative uncharacterized protein
F: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.810, 84.810, 96.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLYchain AAA19 - 21922 - 222
21GLYGLYGLYGLYchain DDD19 - 21922 - 222
12THRTHRLYSLYSchain BBB217 - 2785 - 66
22THRTHRALAALAchain EEE217 - 2755 - 63
13THRTHRLYSLYSchain CCC137 - 1579 - 29
23THRTHRLYSLYSchain FFF137 - 1579 - 29

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Prp38


Mass: 25617.205 Da / Num. of mol.: 2 / Fragment: NTR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0013190 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S1D3
#2: Protein Putative uncharacterized protein


Mass: 10139.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last residue of chain B is modeled as an ALA because only the main chain is visible in the electron density. We are aware that this residue is a LYS.
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0069660 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0SHD7
#3: Protein/peptide Zinc finger domain-containing protein


Mass: 4189.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0035280 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S6R0

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 10 / Details: 0.1 M CAPS, pH 10.0, and 30 % (w/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→42.41 Å / Num. obs: 14056 / % possible obs: 99.8 % / Redundancy: 10.2 % / Rsym value: 0.05 / Net I/σ(I): 21.2
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.2 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RZ9

4rz9


Resolution: 3.1→42.405 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 48.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3473 701 5 %Random selection
Rwork0.2954 13314 --
obs0.2979 14015 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 461.33 Å2 / Biso mean: 230.8469 Å2 / Biso min: 87.25 Å2
Refinement stepCycle: final / Resolution: 3.1→42.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 0 0 4651
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034727
X-RAY DIFFRACTIONf_angle_d0.8456356
X-RAY DIFFRACTIONf_chiral_restr0.034683
X-RAY DIFFRACTIONf_plane_restr0.003838
X-RAY DIFFRACTIONf_dihedral_angle_d15.9771858
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1833X-RAY DIFFRACTION13.658TORSIONAL
12D1833X-RAY DIFFRACTION13.658TORSIONAL
21B507X-RAY DIFFRACTION13.658TORSIONAL
22E507X-RAY DIFFRACTION13.658TORSIONAL
31C196X-RAY DIFFRACTION13.658TORSIONAL
32F196X-RAY DIFFRACTION13.658TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.33930.42131520.39292641279399
3.3393-3.67520.38351440.363826962840100
3.6752-4.20660.38631270.36892669279699
4.2066-5.29830.3641500.334326392789100
5.2983-42.40890.31531280.245926692797100
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)
17.59142.639-0.77013.62882.58063.01130.2201-3.3065-0.91483.2659-0.4118-0.38152.790.20630.87463.43560.63740.47353.43080.42321.273658.4188205.55195.4586
22.30342.3289-2.63866.18780.87416.38870.445-3.95631.02562.74210.4308-1.7102-2.21460.8264-0.26293.82030.7025-0.72193.2393-0.51111.576164.8038222.13640.2977
32.7558-2.14740.63093.0189-0.80661.788-1.5539-4.1969-0.53690.9559-0.43660.0698-1.03360.20061.97591.65230.31130.09162.2518-0.00951.236565.0568212.5836-3.2534
44.0497-3.69553.39236.109-2.59983.0756-1.79690.4920.25633.7681-0.52311.1379-1.31780.39411.91892.59030.729-0.0783.0776-0.86271.920949.5495220.9015-10.7655
54.839-0.14991.44069.27766.25536.8106-0.385-0.77290.76521.23680.49190.7395-1.1084-0.4335-0.06451.13220.5341-0.20671.4953-0.5660.802456.0396213.3907-9.7063
6-0.01030.02930.01380.38420.17020.0803-0.0352-0.71580.08471.0815-0.54952.58560.1041-0.5096-0.15780.46241.93741.37413.6927-0.8420.473546.3201207.4193-12.7278
76.80521.67353.86076.13750.9688.97441.1424-0.3557-3.51581.14230.09040.8092-0.27280.2276-0.13971.40540.71670.28641.8159-0.01371.086959.8971205.1117-14.6585
87.5691.0309-0.88312.10220.22052.50363.1883-0.45691.4874-0.7472-0.43412.34980.8387-0.905-1.94421.55890.0446-0.01352.7656-0.4991.927940.8512199.9552-20.22
98.03383.8662-6.48782.4704-3.3425.29372.01173.3310.2017-2.72540.91452.2577-0.0828-3.4341-2.97012.10960.407-0.1553.51630.72662.341149.0903203.9393-43.9815
103.48233.9687-0.79598.66562.04062.92590.0855-1.047-0.24150.80540.10610.86111.0497-0.48420.1112.2199-0.1596-0.28422.07740.20211.387750.4265196.6538-26.6886
110.7567-0.97860.76352.0383-0.78540.83953.15943.69812.4217-0.0544-1.3807-0.8707-2.6688-2.2218-0.41652.69520.67940.28954.51620.65471.7242.7546164.9079-19.5858
124.1387-0.13482.43937.70151.4655.203-2.57730.4993-0.9846-1.697-1.12151.1183-0.2149-0.53692.60254.00150.61910.11412.371-0.83332.575757.7681232.3714-11.4425
133.6642-4.6735-0.98739.48843.39992.285-0.07253.96710.1823-2.4772-1.72970.52251.0909-0.79581.37362.4997-0.0039-0.04083.0025-0.26461.407963.9131202.3652-68.3696
144.3535-0.762-4.33083.00253.0926.21210.68842.02011.0921-3.0774-0.7428-0.2863-0.50512.72910.09243.1634-0.2941-1.28245.18940.67173.349875.3956216.2925-63.2891
158.8803-1.5056-2.5397.12245.02395.8852-0.27421.55851.256-0.8672-0.3640.0449-0.5651.89370.60131.87330.47230.28252.29520.38130.794771.9789208.1749-57.1209
167.48861.254-0.398.2906-0.84468.2969-0.55220.32920.06520.24180.40940.44311.42151.29260.2810.88460.2290.26451.66020.02370.73666.4513201.5084-49.7459
172.0179-4.0812-5.21964.2417-1.31117.8081-1.1277-1.2845-1.8765-0.77160.1008-2.39282.5262-1.67330.1963.06940.34220.75811.8084-0.05581.82467.6506184.299-42.9675
183.175-0.6118-1.28731.15880.60070.63210.8-2.19150.8980.6050.6120.08392.2004-0.9102-0.80893.13010.496-0.58633.810.26781.207967.2431193.4116-18.9816
191.0467-0.70371.93810.78580.03459.9165-0.1109-0.0113-3.4771.3806-0.07011.02432.71880.22190.20321.4862-0.10110.72781.3477-0.23123.449260.3069191.2674-36.2518
200.6090.3204-0.27631.118-1.24811.41050.0697-1.02190.7262-0.24690.3345-0.12570.15921.88891.2623.04920.8769-2.24362.9107-0.7356.563237.4733167.7603-43.4223
212.15230.8737-1.19032.9265-3.68629.2-0.0418-1.7151-0.58990.7228-0.9613-0.6361-1.73852.10170.39431.9936-0.92280.87414.5133-0.20631.587687.7985215.245-51.4762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 45 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 68 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 98 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 112 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 127 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 141 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 183 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 184 through 202 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 203 through 219 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 217 through 261 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 262 through 278 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 137 through 157 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 19 through 45 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 46 through 68 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 69 through 112 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 113 through 183 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 184 through 202 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 203 through 219 )D0
19X-RAY DIFFRACTION19chain 'E' and (resid 217 through 260 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 261 through 275 )E0
21X-RAY DIFFRACTION21chain 'F' and (resid 137 through 157 )F0

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