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- PDB-6jtg: Structural insights into G domain dimerization and pathogenic mut... -

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Basic information

Entry
Database: PDB / ID: 6jtg
TitleStructural insights into G domain dimerization and pathogenic mutations of OPA1
ComponentsDynamin-like 120 kDa protein, mitochondrial,OPA1 protein
KeywordsHYDROLASE / Mitochondria / fusion / OPA1
Function / homology
Function and homology information


Regulation of Apoptosis / membrane tubulation / inner mitochondrial membrane organization / dynamin GTPase / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion ...Regulation of Apoptosis / membrane tubulation / inner mitochondrial membrane organization / dynamin GTPase / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion / axonal transport of mitochondrion / negative regulation of release of cytochrome c from mitochondria / mitochondrial crista / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / axon cytoplasm / Mitochondrial protein degradation / visual perception / mitochondrion organization / neural tube closure / mitochondrial membrane / mitochondrial intermembrane space / cellular senescence / protein complex oligomerization / microtubule binding / microtubule / mitochondrial outer membrane / mitochondrial inner membrane / GTPase activity / apoptotic process / dendrite / GTP binding / negative regulation of apoptotic process / magnesium ion binding / mitochondrion / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
Dynamin-like 120kDa protein, mitochondrial / Dynamin-like GTPase OPA1, C-terminal / Dynamin-like GTPase OPA1 C-terminal / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / : / Dynamin-like GTPase OPA1, mitochondrial / OPA1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYan, L. / Hu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China20171301816 China
Ministry of Science and Technology (China)2017YFC0840302 China
CitationJournal: J.Cell Biol. / Year: 2020
Title: Structural insights into G domain dimerization and pathogenic mutation of OPA1.
Authors: Yu, C. / Zhao, J. / Yan, L. / Qi, Y. / Guo, X. / Lou, Z. / Hu, J. / Rao, Z.
History
DepositionApr 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynamin-like 120 kDa protein, mitochondrial,OPA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5155
Polymers38,9421
Non-polymers5734
Water2,558142
1
A: Dynamin-like 120 kDa protein, mitochondrial,OPA1 protein
hetero molecules

A: Dynamin-like 120 kDa protein, mitochondrial,OPA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,03010
Polymers77,8852
Non-polymers1,1458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6020 Å2
ΔGint-41 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.890, 77.890, 171.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dynamin-like 120 kDa protein, mitochondrial,OPA1 protein / Optic atrophy protein 1


Mass: 38942.301 Da / Num. of mol.: 1 / Fragment: UNP residues 267-318,UNP residues 254-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPA1 / Production host: Escherichia coli (E. coli)
References: UniProt: O60313, UniProt: Q6PEK6, dynamin GTPase

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium thiocyanate and 20%(w/v) Polyethylene glycol 3350 (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21509 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 20.56
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.345 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.08
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2444 3544 10 %
Rwork0.199 --
obs0.2037 21509 89.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 34 142 2741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092627
X-RAY DIFFRACTIONf_angle_d1.1043553
X-RAY DIFFRACTIONf_dihedral_angle_d4.7011618
X-RAY DIFFRACTIONf_chiral_restr0.061414
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3986-2.43140.4692290.2728267X-RAY DIFFRACTION19
2.4314-2.46620.3519550.295459X-RAY DIFFRACTION33
2.4662-2.5030.3206750.2815676X-RAY DIFFRACTION48
2.503-2.54210.35791050.2668967X-RAY DIFFRACTION68
2.5421-2.58380.30541350.27081187X-RAY DIFFRACTION83
2.5838-2.62830.34021480.25731345X-RAY DIFFRACTION95
2.6283-2.67610.29581600.27381436X-RAY DIFFRACTION99
2.6761-2.72760.32651520.25611384X-RAY DIFFRACTION100
2.7276-2.78320.30221610.24621438X-RAY DIFFRACTION100
2.7832-2.84380.33081580.22791404X-RAY DIFFRACTION100
2.8438-2.90990.28481590.21471444X-RAY DIFFRACTION100
2.9099-2.98270.27251620.21261422X-RAY DIFFRACTION100
2.9827-3.06330.28031600.23431413X-RAY DIFFRACTION100
3.0633-3.15340.2691560.22871429X-RAY DIFFRACTION100
3.1534-3.25520.25641520.20161425X-RAY DIFFRACTION100
3.2552-3.37150.24581570.2011422X-RAY DIFFRACTION100
3.3715-3.50640.19311580.1921413X-RAY DIFFRACTION100
3.5064-3.66590.24291600.17521423X-RAY DIFFRACTION100
3.6659-3.85910.20641550.1761416X-RAY DIFFRACTION100
3.8591-4.10080.2481640.17921425X-RAY DIFFRACTION100
4.1008-4.41720.19221590.16091411X-RAY DIFFRACTION100
4.4172-4.86130.2081530.15021440X-RAY DIFFRACTION100
4.8613-5.56370.20391610.17941419X-RAY DIFFRACTION100
5.5637-7.00580.24521530.19951428X-RAY DIFFRACTION100
7.0058-46.35350.20271570.18241419X-RAY DIFFRACTION100

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