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- PDB-9zmy: Crystal structure of the human Commd10 HN domain in domain swappe... -

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Basic information

Entry
Database: PDB / ID: 9zmy
TitleCrystal structure of the human Commd10 HN domain in domain swapped conformation
ComponentsCOMM domain-containing protein 10
KeywordsEXOCYTOSIS / COMMD / Commander / endosome
Function / homologyCOMM domain-containing protein 10 / COMMD2-7/10, HN domain / COMM domain / COMM domain / COMM domain profile. / Neddylation / nucleoplasm / cytoplasm / COMM domain-containing protein 10
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.619 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 10
B: COMM domain-containing protein 10


Theoretical massNumber of molelcules
Total (without water)26,7932
Polymers26,7932
Non-polymers00
Water1,67593
1
A: COMM domain-containing protein 10

B: COMM domain-containing protein 10


Theoretical massNumber of molelcules
Total (without water)26,7932
Polymers26,7932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area6120 Å2
ΔGint-53 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.624, 59.852, 96.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COMM domain-containing protein 10


Mass: 13396.261 Da / Num. of mol.: 2 / Fragment: HN domain
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 30% PEG400 in 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2025
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.619→48.4 Å / Num. obs: 31360 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 1 / Rpim(I) all: 0.015 / Net I/σ(I): 15.8
Reflection shellResolution: 1.619→1.64 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1141 / CC1/2: 0.82 / Rpim(I) all: 0.521

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
XDSdata reduction
AutoSolphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MAD / Resolution: 1.619→34.173 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 1836 6.42 %
Rwork0.2111 --
obs0.2131 28607 90.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.619→34.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 0 93 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061863
X-RAY DIFFRACTIONf_angle_d0.7132508
X-RAY DIFFRACTIONf_dihedral_angle_d5.8921154
X-RAY DIFFRACTIONf_chiral_restr0.043287
X-RAY DIFFRACTIONf_plane_restr0.005322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.619-1.66250.4145940.36771444X-RAY DIFFRACTION65
1.6625-1.71140.34671180.32741725X-RAY DIFFRACTION78
1.7114-1.76670.33691250.30071799X-RAY DIFFRACTION80
1.7667-1.82980.36161300.2791885X-RAY DIFFRACTION84
1.8298-1.90310.22821430.24191992X-RAY DIFFRACTION89
1.9031-1.98970.28811400.21892043X-RAY DIFFRACTION91
1.9897-2.09450.29981450.22212134X-RAY DIFFRACTION95
2.0945-2.22570.24831510.20742192X-RAY DIFFRACTION97
2.2257-2.39760.28511530.20452221X-RAY DIFFRACTION98
2.3976-2.63870.24091550.21192286X-RAY DIFFRACTION100
2.6387-3.02040.22581580.21132298X-RAY DIFFRACTION100
3.0204-3.80460.21431570.20022319X-RAY DIFFRACTION100
3.8046-34.1730.22561670.19772433X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1907-0.4638-0.09333.93640.45191.1859-0.04740.01810.0878-0.20210.0729-0.0050.2522-0.0378-0.01780.2507-0.03370.00880.27010.00280.221213.236-7.861838.2304
23.0072-1.13721.22385.77490.1792.87170.0380.0951-0.1422-0.40420.1241-0.3014-0.18640.2239-0.13930.243-0.04370.03160.2705-0.04740.197821.384424.304238.1528
31.87790.4915-3.46347.19262.20897.73640.38080.677-0.4424-0.40280.2928-0.71030.26841.329-0.64860.5991-0.12640.00380.8457-0.16850.366123.637987.834224.9466
41.0328-0.09370.44723.8073-0.40421.6705-0.11810.0424-0.14580.03710.19920.0208-0.2025-0.0606-0.07070.2408-0.03830.04770.2649-0.02380.239116.713485.288240.2489
51.4683-1.81510.87887.73-0.71.0572-0.0917-0.41050.53660.39810.1503-1.4335-0.02770.22920.08370.31530.0681-0.09450.3936-0.04580.434223.56853.59543.8895
65.9758-1.21711.80023.24970.44062.85770.11790.35850.6927-0.5422-0.1898-0.24670.10870.0770.02120.3628-0.01720.04430.28020.02490.30514.931655.473232.6747
72.28430.14570.56722.4851-0.1841.72610.07690.05460.1157-0.7642-0.16921.2462-0.019-0.4574-0.010.4266-0.0173-0.15190.3778-0.00550.53622.170152.451233.455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 114 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 6 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 35 )
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 73 )
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 113 )

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