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- PDB-9zn0: Crystal structure of the Commd10 S50E HN domain mutant in domain ... -

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Basic information

Entry
Database: PDB / ID: 9zn0
TitleCrystal structure of the Commd10 S50E HN domain mutant in domain swapped conformation
ComponentsCOMM domain-containing protein 10
KeywordsEXOCYTOSIS / Commander / COMMD / endosome
Function / homology
Function and homology information


Neddylation / nucleoplasm / cytoplasm
Similarity search - Function
COMM domain-containing protein 10 / COMMD2-7/10, HN domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
PENTANOIC ACID / COMM domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsCollins, B.M. / Healy, M.D. / Liu, M. / Hall, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: A remarkable case of conserved domain swapping in the COMMD family of proteins
Authors: Collins, B.M. / Healy, M.D. / Liu, M. / Hall, R.
History
DepositionDec 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMM domain-containing protein 10
B: COMM domain-containing protein 10
C: COMM domain-containing protein 10
D: COMM domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6036
Polymers55,3994
Non-polymers2042
Water2,252125
1
A: COMM domain-containing protein 10
C: COMM domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8023
Polymers27,7002
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-55 kcal/mol
Surface area13230 Å2
MethodPISA
2
B: COMM domain-containing protein 10
D: COMM domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8023
Polymers27,7002
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-51 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.759, 92.173, 59.815
Angle α, β, γ (deg.)90.000, 111.339, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
COMM domain-containing protein 10


Mass: 13849.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD10, HSPC305, PTD002 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6G5
#2: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris (pH 8.5), 0.1 M Mg formate, and 30% PE14/4, with 10% glycerol used as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.12→47.7 Å / Num. obs: 24828 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.45 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 12.7
Reflection shellResolution: 2.12→2.18 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1949 / CC1/2: 0.95 / Rpim(I) all: 0.152

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→40.76 Å / SU ML: 0.1937 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 24.4591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2433 1961 8.06 %
Rwork0.1897 22380 -
obs0.1943 24341 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.96 Å2
Refinement stepCycle: LAST / Resolution: 2.12→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 14 125 3860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443794
X-RAY DIFFRACTIONf_angle_d0.85785105
X-RAY DIFFRACTIONf_chiral_restr0.0468581
X-RAY DIFFRACTIONf_plane_restr0.0111659
X-RAY DIFFRACTIONf_dihedral_angle_d22.97041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.28221360.21781509X-RAY DIFFRACTION91.59
2.17-2.230.2911380.19811557X-RAY DIFFRACTION94.8
2.23-2.30.24371320.19031562X-RAY DIFFRACTION94.43
2.3-2.370.23971400.18421571X-RAY DIFFRACTION96.02
2.37-2.460.2451370.17651580X-RAY DIFFRACTION96.95
2.46-2.550.23491460.17141616X-RAY DIFFRACTION97.46
2.55-2.670.23891420.1931606X-RAY DIFFRACTION97.76
2.67-2.810.29481410.20271615X-RAY DIFFRACTION98.16
2.81-2.990.26521460.20971640X-RAY DIFFRACTION98.67
2.99-3.220.31821380.20221608X-RAY DIFFRACTION98.59
3.22-3.540.25351400.2031638X-RAY DIFFRACTION97.8
3.54-4.050.25071420.17861606X-RAY DIFFRACTION97.65
4.05-5.10.20681400.1671619X-RAY DIFFRACTION96.81
5.1-40.760.21051430.19951653X-RAY DIFFRACTION97.77

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