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- PDB-5f5s: Crystal structure of the Prp38-MFAP1 complex of Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5f5s
TitleCrystal structure of the Prp38-MFAP1 complex of Homo sapiens
Components
  • Microfibrillar-associated protein 1
  • Pre-mRNA-splicing factor 38A
KeywordsSPLICING / B-specific protein / pre-mRNA splicing / SAH
Function / homology
Function and homology information


microfibril / U2-type spliceosomal complex / U2-type precatalytic spliceosome / precatalytic spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / centrosome / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / Pre-mRNA-splicing factor 38 / PRP38 family
Similarity search - Domain/homology
Microfibrillar-associated protein 1 / Pre-mRNA-splicing factor 38A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsUlrich, A.K.C. / 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 / Category: pdbx_audit_support / Item: _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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 38A
B: Microfibrillar-associated protein 1


Theoretical massNumber of molelcules
Total (without water)31,1142
Polymers31,1142
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-3 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.790, 66.790, 242.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Pre-mRNA-splicing factor 38A / Prp38


Mass: 21289.691 Da / Num. of mol.: 1 / Fragment: NTR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF38A / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8NAV1
#2: Protein Microfibrillar-associated protein 1 / MFAP1


Mass: 9824.014 Da / Num. of mol.: 1 / Fragment: UNP residues 267-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MFAP1 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P55081
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.4
Details: 0.1 M sodium acetate, pH 4.4 and 15% (v/v) 1,3-Butandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.24 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.4→57.84 Å / Num. obs: 13389 / % possible obs: 100 % / Redundancy: 18.5 % / Rsym value: 0.072 / Net I/σ(I): 24.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rz9

4rz9


Resolution: 2.4→57.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 25.341 / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.349 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 681 5.1 %RANDOM
Rwork0.2214 ---
obs0.2233 12708 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.6 Å2 / Biso mean: 94.494 Å2 / Biso min: 44.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.59 Å20 Å2
2--1.19 Å20 Å2
3----3.85 Å2
Refinement stepCycle: final / Resolution: 2.4→57.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 0 53 1983
Biso mean---89.78 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191961
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.9782630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5885228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01623.738107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2171521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021474
X-RAY DIFFRACTIONr_mcbond_it2.6367.415918
X-RAY DIFFRACTIONr_mcangle_it4.23611.1041144
X-RAY DIFFRACTIONr_scbond_it4.2497.9091042
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 58 -
Rwork0.346 896 -
all-954 -
obs--100 %
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)
11.5746-0.04430.20630.68280.03790.9991-0.225-0.17360.0138-0.03090.02530.0294-0.0381-0.02740.19970.21850.0891-0.04990.2431-0.0420.0546-13.584-23.23987.3058
21.6246-1.47952.20671.8962-2.66713.8286-0.10230.09040.1089-0.0589-0.1319-0.11780.03410.17530.23430.1919-0.004-0.04220.209-0.03460.105114.3311-20.139617.4224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 176
2X-RAY DIFFRACTION2B270 - 322

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