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- PDB-9m4g: Structure of AtCDC48 N-domain -

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Basic information

Entry
Database: PDB / ID: 9m4g
TitleStructure of AtCDC48 N-domain
ComponentsCell division control protein 48 homolog A
KeywordsPLANT PROTEIN / AAA ATPase / Hexamer / ATP-dependent chaperone / Protein unfollding
Function / homology
Function and homology information


pollen germination / pollen tube growth / negative regulation of defense response / phragmoplast / plant-type cell wall / plasmodesma / lipid droplet / cytosolic ribosome / protein destabilization / spindle ...pollen germination / pollen tube growth / negative regulation of defense response / phragmoplast / plant-type cell wall / plasmodesma / lipid droplet / cytosolic ribosome / protein destabilization / spindle / nuclear envelope / protein transport / cell division / nucleolus / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily ...AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Cell division control protein 48 homolog A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSandholu, A.S. / Zhang, J. / Brandon, Z.H. / Hameed, U.F.S. / Arold, S.T.
Funding support Saudi Arabia, 2items
OrganizationGrant numberCountry
Other privateURF/1/4039-01-01 Saudi Arabia
Other privateURF/1/4080-01-01 Saudi Arabia
CitationJournal: To Be Published
Title: Structure of AtCDC48 N-domain
Authors: Sandholu, A.S. / Zhang, J. / Brandon, Z.H. / Hameed, U.F.S. / Arold, S.T.
History
DepositionMar 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 48 homolog A
B: Cell division control protein 48 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2303
Polymers37,1352
Non-polymers951
Water25214
1
A: Cell division control protein 48 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6622
Polymers18,5671
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-4 kcal/mol
Surface area9030 Å2
MethodPISA
2
B: Cell division control protein 48 homolog A


Theoretical massNumber of molelcules
Total (without water)18,5671
Polymers18,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.716, 91.716, 242.977
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Cell division control protein 48 homolog A / AtCDC48a


Mass: 18567.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDC48A, CDC48, At3g09840, F8A24.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P54609
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 800mM Sodium phosphate monobasic 100mM Potassium phosphate dibasic 100mM Sodium acetate/Acetic Acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.6→48.25 Å / Num. obs: 12475 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 72.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.064 / Rrim(I) all: 0.209 / Net I/σ(I): 10.4
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 21 % / Rmerge(I) obs: 3.143 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1486 / CC1/2: 0.308 / Rpim(I) all: 0.996 / Rrim(I) all: 3.297 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.25 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3189 657 5.27 %
Rwork0.2438 --
obs0.2479 12455 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 5 14 2521
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.014 / Number: 443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.39431300.3682306X-RAY DIFFRACTION100
2.8-3.080.37681290.34172324X-RAY DIFFRACTION100
3.08-3.530.40731080.30732369X-RAY DIFFRACTION100
3.53-4.440.3231410.22972343X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.3353 Å / Origin y: -40.1221 Å / Origin z: 15.1008 Å
111213212223313233
T0.5609 Å2-0.0606 Å20.0865 Å2-0.5919 Å2-0.0193 Å2--0.6651 Å2
L1.8313 °2-0.2283 °21.1707 °2-1.5438 °2-0.3336 °2--2.3249 °2
S0.1164 Å °0.1359 Å °0.3415 Å °-0.1196 Å °-0.0257 Å °-0.2393 Å °-0.0213 Å °0.3068 Å °-0.0613 Å °
Refinement TLS groupSelection details: all

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