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Basic information

Entry
Database: PDB / ID: 6iam
TitleModulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches
Components
  • SER-ALA-ARG-ALA-XY5-VAL-HIS-LEU-ARG-LYS-SER-ALA
  • Small ubiquitin-related modifier 5
  • WD repeat-containing protein 5
KeywordsTRANSFERASE / histone modification / trimethylation at 'Lys-4' / epigenetic transcriptional activation / NSL complex / osteoblasts differentiation / leukemia
Function / homology
Function and homology information


PML body organization / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation ...PML body organization / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / transcription factor binding / Formation of WDR5-containing histone-modifying complexes / ubiquitin-like protein ligase binding / regulation of cell division / regulation of embryonic development / MLL1 complex / protein sumoylation / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / protein tag activity / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / G-protein beta WD-40 repeat ...Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Small ubiquitin-related modifier 5 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsWerel, L. / Essen, L.-O.
CitationJournal: Chembiochem / Year: 2019
Title: Modulating Protein-Protein Interactions with Visible-Light-Responsive Peptide Backbone Photoswitches.
Authors: Albert, L. / Penalver, A. / Djokovic, N. / Werel, L. / Hoffarth, M. / Ruzic, D. / Xu, J. / Essen, L.O. / Nikolic, K. / Dou, Y. / Vazquez, O.
History
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 3.0Jul 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: SER-ALA-ARG-ALA-XY5-VAL-HIS-LEU-ARG-LYS-SER-ALA
C: Small ubiquitin-related modifier 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7768
Polymers35,6123
Non-polymers1635
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-21 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.526, 46.560, 66.168
Angle α, β, γ (deg.)90.000, 107.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 33690.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 28 amino acids were removed / Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61964

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Protein/peptide , 2 types, 2 molecules BC

#2: Protein/peptide SER-ALA-ARG-ALA-XY5-VAL-HIS-LEU-ARG-LYS-SER-ALA


Mass: 1477.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide Small ubiquitin-related modifier 5 / SUMO-5 / SUMO1 pseudogene 1 / Ubiquitin-like 2 / Ubiquitin-like 6


Mass: 444.501 Da / Num. of mol.: 1 / Fragment: UNP residues 5-8
Source method: isolated from a genetically manipulated source
Details: Residual peptide from SUMO-tag, that was cleaved before crystalliisation
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1P1, SUMO5, UBL2, UBL6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2XKQ0

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Non-polymers , 3 types, 428 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.83 % / Description: fine needles
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryosystems 700 series / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 26, 2018 / Details: MD3-UP Microdiffractometer
RadiationMonochromator: U20.2 undulator (14.2 keV) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.51→37.49 Å / Num. obs: 42377 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 11.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0899 / Rpim(I) all: 0.0506 / Rrim(I) all: 0.104 / Χ2: 0.999 / Net I/σ(I): 9.04
Reflection shellResolution: 1.51→1.564 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4073 / CC1/2: 0.617 / Rpim(I) all: 0.414 / Rrim(I) all: 0.827 / Χ2: 0.874 / % possible all: 96.22

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→37.49 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.17 --
Rwork0.148 --
obs-42377 99.33 %
Displacement parametersBiso max: 118.72 Å2 / Biso mean: 18.2115 Å2 / Biso min: 5.41 Å2
Refinement stepCycle: LAST / Resolution: 1.51→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 5 423 2929

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