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- PDB-9n7z: Crystal structure of CT-SLiM-deleted human Drp1 GTPase domain-BSE... -

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Basic information

Entry
Database: PDB / ID: 9n7z
TitleCrystal structure of CT-SLiM-deleted human Drp1 GTPase domain-BSE fusion protein in the apo state
ComponentsDynamin-1-like protein
KeywordsMOTOR PROTEIN / dynamin / Drp1 / mitochondria / GTPase
Function / homology
Function and homology information


mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / peroxisome fission / GTP-dependent protein binding ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / peroxisome fission / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / heart contraction / intracellular distribution of mitochondria / protein complex oligomerization / brush border / clathrin-coated pit / GTPase activator activity / positive regulation of protein secretion / mitochondrion organization / small GTPase binding / synaptic vesicle membrane / endocytosis / calcium ion transport / rhythmic process / peroxisome / regulation of gene expression / microtubule binding / microtubule / mitochondrial outer membrane / GTPase activity / intracellular membrane-bounded organelle / lipid binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / 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
Dynamin-1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsRamachandran, R. / Vahedi-Faridi, A. / Kowatz, T. / Lodowski, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121583 United States
CitationJournal: To Be Published
Title: Crystal structure of CT-SLiM-deleted human Drp1 GTPase domain-BSE fusion protein in the apo state
Authors: Ramachandran, R.
History
DepositionFeb 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-1-like protein
B: Dynamin-1-like protein
C: Dynamin-1-like protein
D: Dynamin-1-like protein


Theoretical massNumber of molelcules
Total (without water)171,7284
Polymers171,7284
Non-polymers00
Water5,549308
1
B: Dynamin-1-like protein
D: Dynamin-1-like protein


Theoretical massNumber of molelcules
Total (without water)85,8642
Polymers85,8642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dynamin-1-like protein


Theoretical massNumber of molelcules
Total (without water)42,9321
Polymers42,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dynamin-1-like protein


Theoretical massNumber of molelcules
Total (without water)42,9321
Polymers42,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.743, 150.611, 87.607
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dynamin-1-like protein / Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less ...Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less / Dymple / Dynamin-like protein / Dynamin-like protein 4 / Dynamin-like protein IV / HdynIV / Dynamin-related protein 1


Mass: 42932.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: delta CT-SLiM GTPase-BSE fusion protein / Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1L, DLP1, DRP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00429, dynamin GTPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Sodium citrate, pH 5.0, 28 % PEG 3000, 6 mg/ml protein, 1:1 ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.51→150.73 Å / Num. obs: 48563 / % possible obs: 100 % / Redundancy: 3.6 % / CC1/2: 0.923 / Rmerge(I) obs: 0.624 / Rpim(I) all: 0.386 / Rrim(I) all: 0.735 / Net I/σ(I): 1.8
Reflection shellResolution: 2.54→2.58 Å / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 3.739 / Num. measured all: 8693 / Num. unique obs: 2414 / CC1/2: 0.338 / Rpim(I) all: 2.301 / Rrim(I) all: 4.399 / Net I/σ(I) obs: 0.2

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Processing

Software
NameVersionClassification
PHENIXdev_5533refinement
DIALSdata scaling
DIALS3.18.0-gbecf27540-releasedata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→32.88 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2903 2204 4.91 %
Rwork0.2433 --
obs0.2457 44864 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10749 0 0 308 11057
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.005 / Number: 1898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.35791060.34172124X-RAY DIFFRACTION75
2.57-2.630.33281040.32542246X-RAY DIFFRACTION82
2.63-2.690.39181420.31322546X-RAY DIFFRACTION92
2.69-2.760.3391410.30492598X-RAY DIFFRACTION95
2.76-2.850.32811380.29842731X-RAY DIFFRACTION98
2.85-2.940.34981400.28952760X-RAY DIFFRACTION100
2.94-3.040.37891270.28372772X-RAY DIFFRACTION100
3.04-3.160.35181360.28042811X-RAY DIFFRACTION99
3.16-3.310.28591410.26992722X-RAY DIFFRACTION100
3.31-3.480.32231390.24452773X-RAY DIFFRACTION99
3.48-3.70.29241390.22512754X-RAY DIFFRACTION99
3.7-3.990.24761390.22012764X-RAY DIFFRACTION99
3.99-4.390.2771400.19832767X-RAY DIFFRACTION99
4.39-5.020.23421550.19152757X-RAY DIFFRACTION99
5.02-6.320.26531670.22462748X-RAY DIFFRACTION99

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