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- PDB-5l7a: The crystal structure of the Human SNF5/INI1 domain -

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Basic information

Entry
Database: PDB / ID: 5l7a
TitleThe crystal structure of the Human SNF5/INI1 domain
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsDNA BINDING PROTEIN / SNF5 INI1 domain crystal
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / npBAF complex / nBAF complex / brahma complex / blastocyst hatching / hepatocyte differentiation / regulation of G0 to G1 transition ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / npBAF complex / nBAF complex / brahma complex / blastocyst hatching / hepatocyte differentiation / regulation of G0 to G1 transition / Tat protein binding / XY body / RNA polymerase I preinitiation complex assembly / RSC-type complex / regulation of nucleotide-excision repair / host-mediated activation of viral transcription / nucleosome disassembly / germ cell nucleus / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / DNA integration / kinetochore / RMTs methylate histone arginines / nuclear matrix / fibrillar center / p53 binding / nervous system development / transcription coactivator activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / SWI/SNF Subunit INI1, DNA binding domain / Chromatin-remodeling complex component Sfh1/SNF5 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsAllen, M.D. / Zinzalla, G. / Bycroft, M.
CitationJournal: FEBS J. / Year: 2018
Title: The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex.
Authors: Sammak, S. / Allen, M.D. / Hamdani, N. / Bycroft, M. / Zinzalla, G.
History
DepositionJun 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Structure summary
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Jan 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

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Assembly

Deposited unit
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
C: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)32,5454
Polymers32,5454
Non-polymers00
Water2,342130
1
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)8,1361
Polymers8,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)8,1361
Polymers8,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)8,1361
Polymers8,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)8,1361
Polymers8,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.619, 73.653, 46.460
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47 / Integrase interactor 1 protein / SNF5 homolog / hSNF5


Mass: 8136.222 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1, BAF47, INI1, SNF5L1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q12824
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 1.4 M tri-sodium citrate and 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. obs: 15711 / % possible obs: 95.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 2.1→2.22 Å / Rmerge(I) obs: 0.438

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L7B

5l7b


Resolution: 2.102→21.419 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 30.77
RfactorNum. reflection% reflection
Rfree0.2602 1395 5.11 %
Rwork0.1995 --
obs0.2026 15656 84.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→21.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 0 130 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082154
X-RAY DIFFRACTIONf_angle_d0.9182920
X-RAY DIFFRACTIONf_dihedral_angle_d12.2521338
X-RAY DIFFRACTIONf_chiral_restr0.051337
X-RAY DIFFRACTIONf_plane_restr0.007380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1019-2.17690.37121520.29332391X-RAY DIFFRACTION79
2.1769-2.2640.35621470.25922418X-RAY DIFFRACTION81
2.264-2.36690.27981460.23912504X-RAY DIFFRACTION81
2.3669-2.49150.33791500.23242489X-RAY DIFFRACTION83
2.4915-2.64740.27181210.23212617X-RAY DIFFRACTION84
2.6474-2.85130.32411250.23252635X-RAY DIFFRACTION85
2.8513-3.13750.26841350.21572663X-RAY DIFFRACTION87
3.1375-3.58960.30311380.19212670X-RAY DIFFRACTION87
3.5896-4.51560.19831430.16182730X-RAY DIFFRACTION89
4.5156-21.42020.1981380.16572777X-RAY DIFFRACTION91

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