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- PDB-6vpq: Crystal structure of the C-terminal domain of DENR -

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Basic information

Entry
Database: PDB / ID: 6vpq
TitleCrystal structure of the C-terminal domain of DENR
ComponentsDensity-regulated protein
KeywordsTRANSLATION / protein synthesis regulation / translation initiation / translation reinitiation / translation recycling / density regulated protein (DENR)
Function / homology
Function and homology information


IRES-dependent viral translational initiation / translation reinitiation / formation of translation preinitiation complex / ribosome disassembly / translation initiation factor activity / cytoplasm
Similarity search - Function
DENR family, eukaryotes / DENR, C-terminal domain / : / DENR, N-terminal / : / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Density-regulated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLomakin, I.B. / Steitz, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2020
Title: Crystal structure of the C-terminal domain of DENR.
Authors: Lomakin, I.B. / De, S. / Wang, J. / Borkar, A.N. / Steitz, T.A.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Density-regulated protein
B: Density-regulated protein
C: Density-regulated protein
D: Density-regulated protein
E: Density-regulated protein
F: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,34946
Polymers132,8406
Non-polymers2,50840
Water8,791488
1
A: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5978
Polymers22,1401
Non-polymers4577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6029
Polymers22,1401
Non-polymers4628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6797
Polymers22,1401
Non-polymers5396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3795
Polymers22,1401
Non-polymers2394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3635
Polymers22,1401
Non-polymers2234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72912
Polymers22,1401
Non-polymers58911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.670, 47.260, 95.500
Angle α, β, γ (deg.)90.000, 106.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Density-regulated protein / DRP / Protein DRP1 / Smooth muscle cell-associated protein 3 / SMAP-3


Mass: 22140.047 Da / Num. of mol.: 6 / Mutation: fragment, aa 110-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DENR, DRP1, H14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43583

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Non-polymers , 5 types, 528 molecules

#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M CaCl2, 15% PEG 400, 0.1 M Sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.74→91.667 Å / Num. obs: 56630 / % possible obs: 98.9 % / Redundancy: 4.398 % / Biso Wilson estimate: 36.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.121 / Χ2: 1.017 / Net I/σ(I): 7.84 / Num. measured all: 249082 / Scaling rejects: 335
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
1.74-1.794.3636.5960.1818055416541387.50599.4
1.79-1.834.1873.9550.3217167411741004.52799.60.116
1.83-1.894.6322.6740.5318469399339873.02199.80.241
1.89-1.954.6091.7480.817684385038371.97599.70.341
1.95-2.014.5141.2941.1316965376837581.46899.70.477
2.01-2.084.4571.0071.5116191365236331.14499.50.645
2.08-2.164.1980.7212.1314661351534920.82699.30.754
2.16-2.254.2590.4863.1714243336933440.55599.30.876
2.25-2.354.5790.3974.1714644322231980.45199.30.908
2.35-2.464.4790.2995.5213737310830670.34198.70.932
2.46-2.594.4470.2426.8313055299729360.276980.946
2.59-2.754.2420.1858.7411539277427200.21498.10.96
2.75-2.944.280.12712.6311145264226040.14898.60.976
2.94-3.184.6420.10117.3211332244624410.11699.80.984
3.18-3.484.5460.07421.5910119225522260.08698.70.99
3.48-3.894.3250.05326.168663205620030.06297.40.993
3.89-4.494.0540.04328.077192182617740.04997.20.996
4.49-5.54.3620.03732.156692156115340.04298.30.997
5.5-7.784.1410.03630.964857121711730.04296.40.997
7.78-91.6674.0180.0335.8826727046650.03594.50.998

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VYC

5vyc


Resolution: 1.74→91.667 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.86
RfactorNum. reflection% reflection
Rfree0.2473 2406 4.7 %
Rwork0.1781 --
obs0.1812 51222 89.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157 Å2 / Biso mean: 48.5637 Å2 / Biso min: 18.47 Å2
Refinement stepCycle: final / Resolution: 1.74→91.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 145 490 4745
Biso mean--77.41 55.47 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7401-1.77560.7417240.645840313
1.7756-1.81420.5195580.4556111736
1.8142-1.85640.40591500.3847285690
1.8564-1.90280.381660.3444316199
1.9028-1.95430.35751460.315313999
1.9543-2.01180.34991670.29483168100
2.0118-2.07670.31041580.2798316899
2.0767-2.1510.34261680.2653319099
2.151-2.23710.31171620.2461314299
2.2371-2.33890.31411220.2283321899
2.3389-2.46220.33371460.2148314899
2.4622-2.61650.3041630.214314198
2.6165-2.81850.30411950.2083310398
2.8185-3.10220.22211500.17253223100
3.1022-3.55110.23511600.1464319899
3.5511-4.4740.17391270.124317697
4.474-91.60.17991440.1315326597
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)
12.8833-0.48150.03762.678-0.09645.3459-0.0863-0.3425-0.01820.3880.1188-0.1999-0.24680.1917-0.03490.2960.0423-0.0450.3251-0.0190.2469.1905-22.9467-9.3853
23.3963-0.834-0.00774.239-0.00823.9037-0.0748-0.07050.24720.1075-0.0278-0.1811-0.24730.08060.08950.2233-0.0037-0.00120.1854-0.00250.2096-2.2766-5.6625-24.4565
34.5413-0.5161-1.06963.59660.27723.3131-0.0982-0.158-0.05690.27540.08470.5650.0614-0.31820.0280.25380.02910.00070.25090.00210.3519-14.398-27.2896-19.1215
43.7840.62780.30583.66130.48113.9069-0.1760.0333-0.2855-0.0444-0.0240.15660.0675-0.31110.1790.30420.00640.0440.2498-0.02150.3816-37.8863-14.7022-33.5598
54.243-1.0533-2.28073.40240.84584.6745-0.0207-0.11660.13650.07680.24660.0488-0.2182-0.2504-0.19480.24020.05340.04390.3217-0.00250.2919-38.06466.1987-18.9803
64.6554-1.04981.21483.1644-1.58024.999-0.03610.0231-0.0922-0.05680.0341-0.02830.09080.15670.00230.22160.0045-0.00630.2074-0.01080.1807-27.50436.9047-42.4609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and resid 128:195 or (chain 'C' and resid 113:122)A0
2X-RAY DIFFRACTION2chain 'B' and resid 128:195 or (chain 'A' and resid 113:122)B0
3X-RAY DIFFRACTION3chain 'C' and resid 128:195 or (chain 'B' and resid 113:122)C0
4X-RAY DIFFRACTION4chain 'D' and resid 128:195 or (chain 'F' and resid 113:122)D0
5X-RAY DIFFRACTION5chain 'E' and resid 128:195 or (chain 'D' and resid 113:122)E0
6X-RAY DIFFRACTION6chain 'F' and resid 128:195 or (chain 'E' and resid 113:122)F0

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