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- PDB-8b9x: Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 -

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Basic information

Entry
Database: PDB / ID: 8b9x
TitleChimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1
ComponentsDDRGK domain-containing protein 1,E3 UFM1-protein ligase 1
KeywordsSIGNALING PROTEIN / post-translational modification / E3 ligases
Function / homology
Function and homology information


UFM1 ligase activity / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation ...UFM1 ligase activity / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of intracellular estrogen receptor signaling pathway / positive regulation of proteasomal protein catabolic process / Transferases; Acyltransferases; Aminoacyltransferases / cartilage development / regulation of canonical NF-kappaB signal transduction / reticulophagy / response to L-glutamate / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RHOA GTPase cycle / hematopoietic stem cell differentiation / positive regulation of autophagy / positive regulation of glial cell proliferation / negative regulation of protein ubiquitination / response to endoplasmic reticulum stress / erythrocyte differentiation / DNA damage checkpoint signaling / regulation of protein stability / osteoblast differentiation / regulation of protein localization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / positive regulation of cell migration / neuron projection / negative regulation of gene expression / DNA repair / DNA damage response / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
DDRGK domain containing protein / DDRGK domain / DDRGK / E3 UFM1-protein ligase 1 / E3 UFM1-protein ligase 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 UFM1-protein ligase 1 / DDRGK domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.066 Å
AuthorsWiener, R. / Isupov, M. / banerjee, S.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation491/21 Israel
CitationJournal: Embo Rep. / Year: 2023
Title: Structural study of UFL1-UFC1 interaction uncovers the role of UFL1 N-terminal helix in ufmylation.
Authors: Banerjee, S. / Varga, J.K. / Kumar, M. / Zoltsman, G. / Rotem-Bamberger, S. / Cohen-Kfir, E. / Isupov, M.N. / Rosenzweig, R. / Schueler-Furman, O. / Wiener, R.
History
DepositionOct 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1
B: DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8234
Polymers61,7522
Non-polymers712
Water181
1
A: DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9122
Polymers30,8761
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9122
Polymers30,8761
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.568, 145.568, 83.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 0 - 253 / Label seq-ID: 1 - 254

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1 / Dashurin / UFM1-binding and PCI domain-containing protein 1 / E3 UFM1-protein transferase 1 / ...Dashurin / UFM1-binding and PCI domain-containing protein 1 / E3 UFM1-protein transferase 1 / Multiple alpha-helix protein located at ER / Novel LZAP-binding protein / Regulator of C53/LZAP and DDRGK1


Mass: 30876.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: DDRGK1, C20orf116, UFBP1, UFL1, KIAA0776, MAXER, NLBP, RCAD
Production host: Escherichia coli (E. coli)
References: UniProt: Q96HY6, UniProt: O94874, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.42 Å3/Da / Density % sol: 72.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Sodium acetate trihydrate Ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.066→63.112 Å / Num. obs: 18967 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.997 / Net I/σ(I): 8.7
Reflection shellResolution: 3.066→3.28 Å / Num. unique obs: 3414 / CC1/2: 0.446

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
PARROTphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 3.066→63.112 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.221 / Average fsc free: 0.7395 / Average fsc work: 0.7535 / Cross valid method: FREE R-VALUE / ESU R: 1.119 / ESU R Free: 0.404 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2723 936 4.938 %
Rwork0.2326 18020 -
all0.235 --
obs-18956 99.716 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 123.573 Å2
Baniso -1Baniso -2Baniso -3
1--1.579 Å2-0.789 Å2-0 Å2
2---1.579 Å2-0 Å2
3---5.122 Å2
Refinement stepCycle: LAST / Resolution: 3.066→63.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4041 0 2 1 4044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124118
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.6275568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22522.963243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95715787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7911534
X-RAY DIFFRACTIONr_chiral_restr0.0590.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023057
X-RAY DIFFRACTIONr_nbd_refined0.2190.21595
X-RAY DIFFRACTIONr_nbtor_refined0.2830.22890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3760.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.23
X-RAY DIFFRACTIONr_mcbond_it8.71311.8632050
X-RAY DIFFRACTIONr_mcangle_it11.7717.8612561
X-RAY DIFFRACTIONr_scbond_it10.82412.5952068
X-RAY DIFFRACTIONr_scangle_it14.9318.6983003
X-RAY DIFFRACTIONr_lrange_it16.847162.4495819
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.057674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.100250.05008
12BX-RAY DIFFRACTIONLocal ncs0.100250.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.066-3.1460.355750.3641291X-RAY DIFFRACTION97.9914
3.146-3.2320.391760.3631291X-RAY DIFFRACTION100
3.232-3.3260.408490.3561283X-RAY DIFFRACTION100
3.326-3.4280.497490.3631224X-RAY DIFFRACTION100
3.428-3.540.352520.3551183X-RAY DIFFRACTION100
3.54-3.6650.407490.3131162X-RAY DIFFRACTION100
3.665-3.8030.346640.2931117X-RAY DIFFRACTION100
3.803-3.9580.31490.2861071X-RAY DIFFRACTION99.9108
3.958-4.1340.315710.254999X-RAY DIFFRACTION100
4.134-4.3350.365460.255984X-RAY DIFFRACTION100
4.335-4.5690.261540.254923X-RAY DIFFRACTION100
4.569-4.8460.283500.227870X-RAY DIFFRACTION98.5011
4.846-5.180.308510.221811X-RAY DIFFRACTION99.4233
5.18-5.5950.261440.224784X-RAY DIFFRACTION100
5.595-6.1270.43250.232719X-RAY DIFFRACTION100
6.127-6.8480.261380.232644X-RAY DIFFRACTION100
6.848-7.9040.272330.184571X-RAY DIFFRACTION100
7.904-9.6710.129330.117481X-RAY DIFFRACTION99.8058
9.671-13.6370.083160.111391X-RAY DIFFRACTION100
13.637-63.1120.264120.303221X-RAY DIFFRACTION97.8992

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