[English] 日本語
Yorodumi
- PDB-5f5v: Crystal structure of the Snu23-Prp38-MFAP1(217-296) complex of Ch... -

+
Open data


ID or keywords:

Loading...

-
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


U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more