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- PDB-6h77: E1 enzyme for ubiquitin like protein activation in complex with UBL -

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Basic information

Entry
Database: PDB / ID: 6h77
TitleE1 enzyme for ubiquitin like protein activation in complex with UBL
Components
  • Ubiquitin-fold modifier 1
  • Ubiquitin-like modifier-activating enzyme 5
KeywordsSIGNALING PROTEIN / Ubiquitin like protein activating enzyme
Function / homology
Function and homology information


UFM1 activating enzyme activity / protein K69-linked ufmylation / protein ufmylation / megakaryocyte differentiation / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / response to endoplasmic reticulum stress ...UFM1 activating enzyme activity / protein K69-linked ufmylation / protein ufmylation / megakaryocyte differentiation / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / response to endoplasmic reticulum stress / erythrocyte differentiation / brain development / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / zinc ion binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain ...Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Ubiquitin-fold modifier 1 / Ubiquitin-like modifier-activating enzyme 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSoudah, N. / Padala, P. / Hassouna, F. / Mashahreh, B. / Lebedev, A.A. / Isupov, M.N. / Cohen-Kfir, E. / Wiener, R.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation.
Authors: Soudah, N. / Padala, P. / Hassouna, F. / Kumar, M. / Mashahreh, B. / Lebedev, A.A. / Isupov, M.N. / Cohen-Kfir, E. / Wiener, R.
History
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme 5
B: Ubiquitin-like modifier-activating enzyme 5
C: Ubiquitin-like modifier-activating enzyme 5
D: Ubiquitin-like modifier-activating enzyme 5
Q: Ubiquitin-fold modifier 1
R: Ubiquitin-fold modifier 1
S: Ubiquitin-fold modifier 1
T: Ubiquitin-fold modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,81762
Polymers171,8418
Non-polymers4,97654
Water9,278515
1
A: Ubiquitin-like modifier-activating enzyme 5
B: Ubiquitin-like modifier-activating enzyme 5
Q: Ubiquitin-fold modifier 1
T: Ubiquitin-fold modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,28030
Polymers85,9214
Non-polymers2,36026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18440 Å2
ΔGint-78 kcal/mol
Surface area29890 Å2
MethodPISA
2
C: Ubiquitin-like modifier-activating enzyme 5
D: Ubiquitin-like modifier-activating enzyme 5
R: Ubiquitin-fold modifier 1
S: Ubiquitin-fold modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,53632
Polymers85,9214
Non-polymers2,61628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19110 Å2
ΔGint-76 kcal/mol
Surface area29200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.110, 105.520, 93.880
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17Q
27R
18Q
28S
19Q
29T
110R
210S
111R
211T
112S
212T

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVALAA36 - 3461 - 311
21GLYGLYVALVALBB36 - 3461 - 311
12GLYGLYVALVALAA36 - 3461 - 311
22GLYGLYVALVALCC36 - 3461 - 311
13GLYGLYVALVALAA36 - 3461 - 311
23GLYGLYVALVALDD36 - 3461 - 311
14GLYGLYVALVALBB36 - 3461 - 311
24GLYGLYVALVALCC36 - 3461 - 311
15GLYGLYVALVALBB36 - 3461 - 311
25GLYGLYVALVALDD36 - 3461 - 311
16GLYGLYVALVALCC36 - 3461 - 311
26GLYGLYVALVALDD36 - 3461 - 311
17METMETPROPROQE1 - 781 - 78
27METMETPROPRORF1 - 781 - 78
18METMETPROPROQE1 - 781 - 78
28METMETPROPROSG1 - 781 - 78
19METMETPROPROQE1 - 781 - 78
29METMETPROPROTH1 - 781 - 78
110METMETPROPRORF1 - 781 - 78
210METMETPROPROSG1 - 781 - 78
111METMETPROPRORF1 - 781 - 78
211METMETPROPROTH1 - 781 - 78
112METMETPROPROSG1 - 781 - 78
212METMETPROPROTH1 - 781 - 78

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules ABCDQRST

#1: Protein
Ubiquitin-like modifier-activating enzyme 5 / Ubiquitin-activating enzyme 5 / ThiFP1 / UFM1-activating enzyme / Ubiquitin-activating enzyme E1 ...Ubiquitin-activating enzyme 5 / ThiFP1 / UFM1-activating enzyme / Ubiquitin-activating enzyme E1 domain-containing protein 1


Mass: 34607.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9
#2: Protein
Ubiquitin-fold modifier 1


Mass: 8352.673 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFM1, C13orf20, BM-002 / Production host: Escherichia coli (E. coli) / References: UniProt: P61960

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Non-polymers , 6 types, 569 molecules

#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→58.53 Å / Num. obs: 92451 / % possible obs: 98.5 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 1.814 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.517

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H78

6h78


Resolution: 2.1→52.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.475 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.22089 2369 2.5 %RANDOM
Rwork0.18401 ---
obs0.18492 92451 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.119 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20.2 Å2
2--6.49 Å20 Å2
3----3.68 Å2
Refinement stepCycle: 1 / Resolution: 2.1→52.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11700 0 297 515 12512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01212653
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.65917104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56551629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19123.046627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.042152186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9991572
X-RAY DIFFRACTIONr_chiral_restr0.110.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029316
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.84913.2976182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.05522.2957738
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it11.56614.9446471
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.06995.97851491
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A96450.08
12B96450.08
21A96020.08
22C96020.08
31A95950.08
32D95950.08
41B96890.07
42C96890.07
51B96580.07
52D96580.07
61C96380.07
62D96380.07
71Q24120.05
72R24120.05
81Q24100.06
82S24100.06
91Q23890.05
92T23890.05
101R23870.07
102S23870.07
111R23780.06
112T23780.06
121S23820.05
122T23820.05
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 136 -
Rwork0.364 6712 -
obs--96.48 %

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