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- PDB-9zmz: Crystal structure of the human Commd4 HN domain in a domain swapp... -

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Basic information

Entry
Database: PDB / ID: 9zmz
TitleCrystal structure of the human Commd4 HN domain in a domain swapped conformation
ComponentsCOMM domain-containing protein 4
KeywordsPROTEIN TRANSPORT / COMMD / endosome / Commander
Function / homology
Function and homology information


Neddylation / intracellular membrane-bounded organelle / signal transduction / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
COMM domain-containing protein 4 / : / COMMD2-7/10, HN domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
COMM domain-containing protein 4
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

Downloads & links

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Assembly

Deposited unit
A: COMM domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)12,2721
Polymers12,2721
Non-polymers00
Water23413
1
A: COMM domain-containing protein 4

A: COMM domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)24,5442
Polymers24,5442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6110 Å2
ΔGint-60 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.535, 51.535, 79.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

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Components

#1: Protein COMM domain-containing protein 4


Mass: 12272.179 Da / Num. of mol.: 1 / Fragment: HN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0A8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M Tris (pH 8.0) and 28% PEG4000

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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→44.63 Å / Num. obs: 7291 / % possible obs: 99.6 % / Redundancy: 19.1 % / Biso Wilson estimate: 47.17 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 16.4
Reflection shellResolution: 2.12→2.18 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 562 / CC1/2: 0.494 / Rpim(I) all: 0.361

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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→44.63 Å / SU ML: 0.274 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 38.8647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3043 701 10.02 %
Rwork0.2298 6293 -
obs0.2371 6994 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.63 Å2
Refinement stepCycle: LAST / Resolution: 2.12→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 0 0 13 764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0298758
X-RAY DIFFRACTIONf_angle_d2.52241019
X-RAY DIFFRACTIONf_chiral_restr0.1274125
X-RAY DIFFRACTIONf_plane_restr0.0188125
X-RAY DIFFRACTIONf_dihedral_angle_d23.8525283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.280.37091310.25141107X-RAY DIFFRACTION86.69
2.29-2.510.28821320.23661235X-RAY DIFFRACTION95.66
2.52-2.880.33141410.28871266X-RAY DIFFRACTION97.51
2.88-3.620.32821460.26471302X-RAY DIFFRACTION99.25
3.63-44.630.28591510.20091383X-RAY DIFFRACTION99.74

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