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- PDB-6bp6: Crystal structure of Commd9 COMM domain -

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Basic information

Entry
Database: PDB / ID: 6bp6
TitleCrystal structure of Commd9 COMM domain
ComponentsCOMM domain-containing protein 9
KeywordsENDOCYTOSIS / Copper metabolism / COMM domain / CCC complex / Commander complex / membrane trafficking / recycling / Retriever / endosome
Function / homology
Function and homology information


sodium ion transport / cholesterol homeostasis / Neddylation / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / Golgi apparatus / extracellular region / nucleoplasm / cytosol
Similarity search - Function
COMM domain-containing protein 9 / : / COMMD9, helical N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
COMM domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsHealy, M.D. / Chandra, M. / Collins, B.M. / Ghai, R.
Funding support Australia, 5items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1097185 Australia
University of Queensland2016003796 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1058734 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1061574 Australia
Australian Research Council (ARC)DP160101743 Australia
CitationJournal: Elife / Year: 2018
Title: Structural insights into the architecture and membrane interactions of the conserved COMMD proteins.
Authors: Healy, M.D. / Hospenthal, M.K. / Hall, R.J. / Chandra, M. / Chilton, M. / Tillu, V. / Chen, K.E. / Celligoi, D.J. / McDonald, F.J. / Cullen, P.J. / Lott, J.S. / Collins, B.M. / Ghai, R.
History
DepositionNov 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMM domain-containing protein 9
B: COMM domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)21,1452
Polymers21,1452
Non-polymers00
Water1629
1
A: COMM domain-containing protein 9
B: COMM domain-containing protein 9

A: COMM domain-containing protein 9
B: COMM domain-containing protein 9

A: COMM domain-containing protein 9
B: COMM domain-containing protein 9

A: COMM domain-containing protein 9
B: COMM domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)84,5808
Polymers84,5808
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area24190 Å2
ΔGint-187 kcal/mol
Surface area34290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.404, 79.404, 58.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-107-

HOH

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Components

#1: Protein COMM domain-containing protein 9


Mass: 10572.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD9, HSPC166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P000
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES (pH 7.0), 6% Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.17→47.13 Å / Num. obs: 9689 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.7
Reflection shellResolution: 2.17→2.24 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2954: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→30.366 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2855 950 9.97 %
Rwork0.2477 --
obs0.2514 9527 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→30.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 0 9 1247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041248
X-RAY DIFFRACTIONf_angle_d0.6371682
X-RAY DIFFRACTIONf_dihedral_angle_d15.906792
X-RAY DIFFRACTIONf_chiral_restr0.043212
X-RAY DIFFRACTIONf_plane_restr0.005208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1699-2.28430.39061300.30891135X-RAY DIFFRACTION93
2.2843-2.42730.39261330.31321211X-RAY DIFFRACTION96
2.4273-2.61470.36211300.30871207X-RAY DIFFRACTION98
2.6147-2.87760.35751370.29851250X-RAY DIFFRACTION99
2.8776-3.29360.32171450.28251239X-RAY DIFFRACTION100
3.2936-4.14790.27951350.25371264X-RAY DIFFRACTION100
4.1479-30.36870.23831400.20691271X-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)
14.2567-1.38111.95964.04552.49581.29530.36830.2517-0.132-0.90620.03820.6938-0.05170.1851-0.4560.407-0.09690.05930.4874-0.02570.407822.682428.76089.8432
23.1914-2.69761.09122.3193-1.01310.5291-2.9486-0.89270.14682.61860.9070.1588-0.15820.72520.51481.55720.62440.72372.16370.03851.111723.58317.904328.1843
36.20912.2614-2.288.9196-1.31396.18810.06780.25610.67050.06280.25250.6519-1.21090.1677-0.05660.62170.0158-0.0260.6662-0.07090.608825.35629.411911.3658
46.4471-2.74391.12675.725-6.07994.8896-0.0631-1.0009-0.4701-0.2020.68461.43280.2012-0.6128-0.76120.5117-0.07320.00440.7251-0.14261.00087.003537.656516.2017
53.6776-1.08280.10850.21550.02250.1396-3.937-1.4297-2.82432.71631.51361.27944.1567-0.47440.50931.90130.34050.92560.09130.55971.325432.09418.015522.8436
65.103-5.27592.85095.2091-2.33086.4339-0.2734-0.0969-0.14740.8510.140.93960.02920.0815-0.06080.4591-0.00660.14660.5381-0.01820.703716.436541.533718.5567
70.2712-1.7338-0.66251.99250.8822.0513-0.11493.80471.19381.6541-1.71951.97890.0245-6.02570.2731.1836-0.2397-0.04272.15040.48131.4068.702555.12510.66
88.7914-2.19364.17797.3860.25562.84270.31260.8241-0.69590.2119-0.37480.41530.63690.79930.21420.5588-0.03250.06640.51970.01180.6818.449240.844316.6661
99.1485-2.12550.61736.9714-0.36627.8297-0.61190.60110.92980.5141-0.287-1.20420.03352.42980.05120.5194-0.0345-0.05260.625-0.10640.57125.648436.821218.6985
103.4117-2.91553.53134.0891-0.14484.96550.61091.3475-1.3391-1.6436-0.3182.32190.76740.0111-0.31730.5334-0.0251-0.03840.6274-0.07931.316112.953520.792412.013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 29 )
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 8 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 21 )
7X-RAY DIFFRACTION7chain 'B' and (resid 22 through 29 )
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 89 )

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