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- PDB-8f6d: Crystal structure of the CNNM2 CBS-pair domain in complex with ARL15 -

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Basic information

Entry
Database: PDB / ID: 8f6d
TitleCrystal structure of the CNNM2 CBS-pair domain in complex with ARL15
Components
  • ADP-ribosylation factor-like protein 15
  • Metal transporter CNNM2
KeywordsPROTEIN BINDING / Protein complex / cation transport
Function / homology
Function and homology information


magnesium ion homeostasis / magnesium ion transmembrane transporter activity / basolateral plasma membrane / GTPase activity / GTP binding / extracellular exosome / ATP binding / plasma membrane
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor ...Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / RmlC-like jelly roll fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Metal transporter CNNM2 / ADP-ribosylation factor-like protein 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKozlov, G. / Mahbub, L. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Elife / Year: 2023
Title: Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15.
Authors: Mahbub, L. / Kozlov, G. / Zong, P. / Lee, E.L. / Tetteh, S. / Nethramangalath, T. / Knorn, C. / Jiang, J. / Shahsavan, A. / Yue, L. / Runnels, L. / Gehring, K.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal transporter CNNM2
B: ADP-ribosylation factor-like protein 15
C: Metal transporter CNNM2
D: ADP-ribosylation factor-like protein 15
E: Metal transporter CNNM2
F: ADP-ribosylation factor-like protein 15
G: Metal transporter CNNM2
H: ADP-ribosylation factor-like protein 15


Theoretical massNumber of molelcules
Total (without water)149,2828
Polymers149,2828
Non-polymers00
Water0
1
A: Metal transporter CNNM2
B: ADP-ribosylation factor-like protein 15


Theoretical massNumber of molelcules
Total (without water)37,3202
Polymers37,3202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Metal transporter CNNM2
D: ADP-ribosylation factor-like protein 15


Theoretical massNumber of molelcules
Total (without water)37,3202
Polymers37,3202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Metal transporter CNNM2
F: ADP-ribosylation factor-like protein 15


Theoretical massNumber of molelcules
Total (without water)37,3202
Polymers37,3202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Metal transporter CNNM2
H: ADP-ribosylation factor-like protein 15


Theoretical massNumber of molelcules
Total (without water)37,3202
Polymers37,3202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.018, 73.323, 79.327
Angle α, β, γ (deg.)94.353, 95.500, 115.330
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 434 or (resid 435 through 436...
d_2ens_1(chain "C" and (resid 434 or (resid 435 through 436...
d_3ens_1(chain "E" and (resid 434 or (resid 435 through 436...
d_4ens_1(chain "G" and (resid 434 through 447 or (resid 448...
d_1ens_2(chain "B" and ((resid 34 and (name N or name...
d_2ens_2(chain "D" and (resid 34 through 36 or (resid 37...
d_3ens_2(chain "F" and ((resid 34 and (name N or name...
d_4ens_2(chain "H" and (resid 34 through 37 or (resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEVALA6 - 123
d_12ens_1PHELEUA130 - 152
d_21ens_1ILEVALC1 - 118
d_22ens_1PHELEUC122 - 144
d_31ens_1ILEVALE5 - 122
d_32ens_1PHELEUE124 - 146
d_41ens_1ILELEUG2 - 142
d_11ens_2ASPLEUB2 - 17
d_12ens_2ASNASNB29
d_13ens_2GLULEUB32 - 57
d_14ens_2SERLEUB59 - 90
d_15ens_2SERSERB97 - 122
d_16ens_2METLEUB126 - 140
d_21ens_2ASPLEUD3 - 18
d_22ens_2ASNASND30
d_23ens_2GLULEUD33 - 58
d_24ens_2SERLEUD60 - 91
d_25ens_2SERSERD102 - 127
d_26ens_2METLEUD130 - 144
d_31ens_2ASPLEUF1 - 16
d_32ens_2ASNASNF27
d_33ens_2GLULEUF29 - 54
d_34ens_2SERLEUF56 - 87
d_35ens_2SERSERF96 - 121
d_36ens_2METLEUF123 - 137
d_41ens_2ASPLEUH2 - 17
d_42ens_2ASNASNH27
d_43ens_2GLULEUH30 - 87
d_44ens_2SERSERH91 - 116
d_45ens_2METLEUH118 - 132

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.72718306536, -0.493228981999, -0.477420109306), (-0.475088557443, -0.140386653494, 0.868667053656), (-0.495475178027, 0.85849680188, -0.132240648524)51.024973898, 40.4501111191, -12.0045042926
2given(-0.716988738678, -0.480828047824, -0.504709358972), (-0.312177702233, -0.425887296299, 0.849214397593), (-0.623275405288, 0.766436167778, 0.155252600254)70.4799323072, 11.3013334348, -41.1746285635
3given(0.999941915405, -0.0100710757701, -0.00383917300008), (0.00830317787938, 0.946917991519, -0.321367973784), (0.0068719032004, 0.321317429919, 0.946946612105)21.298184921, -31.9114951669, -43.6535739272
4given(-0.740722040147, -0.454241936694, -0.494969819473), (-0.484341556851, -0.149495936765, 0.862011729153), (-0.465557854136, 0.878245539607, -0.109273311531)51.4240002127, 40.5560000077, -12.4873316269
5given(-0.718147873295, -0.465746596433, -0.517052937322), (-0.309617562675, -0.451566746952, 0.836794143103), (-0.623217936973, 0.761030604482, 0.180088372962)70.7721105633, 10.9516979051, -41.113783972
6given(0.998857487284, -0.0439461501968, 0.0187738109942), (0.0474521337463, 0.958603394302, -0.280762938146), (-0.00565818869357, 0.281333020309, 0.959593516331)21.3875141514, -32.2426738523, -43.4290454033

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Components

#1: Protein
Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / Cyclin-M2


Mass: 17864.365 Da / Num. of mol.: 4 / Fragment: CBS 1 and CBS 2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM2, ACDP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M5
#2: Protein
ADP-ribosylation factor-like protein 15 / ADP-ribosylation factor-related protein 2 / ARF-related protein 2


Mass: 19456.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL15, ARFRP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NXU5

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M Tris pH 8.5, 25% (w/v) PEG3350, 0.5 mM GppNp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 20526 / % possible obs: 94.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 114.46 Å2 / CC1/2: 0.998 / Rsym value: 0.078 / Net I/σ(I): 10.4
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1986 / CC1/2: 0.624 / Rsym value: 0.782 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IY0

4iy0


Resolution: 3.2→29.53 Å / SU ML: 0.6467 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.0886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2927 1027 5 %
Rwork0.2641 19499 -
obs0.2655 20526 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.3 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7791 0 0 0 7791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00377911
X-RAY DIFFRACTIONf_angle_d0.790610835
X-RAY DIFFRACTIONf_chiral_restr0.04711368
X-RAY DIFFRACTIONf_plane_restr0.00651396
X-RAY DIFFRACTIONf_dihedral_angle_d3.9661157
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.847732657002
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.863052682937
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.0040478446
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.833275927917
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.44460084713
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS1.32087835788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.370.3831430.36032689X-RAY DIFFRACTION90.22
3.37-3.580.3671390.33122653X-RAY DIFFRACTION88.86
3.58-3.860.35791500.28942873X-RAY DIFFRACTION96.71
3.86-4.240.33481490.27082814X-RAY DIFFRACTION96.08
4.24-4.850.31681480.26422819X-RAY DIFFRACTION94.67
4.85-6.110.32351480.27082798X-RAY DIFFRACTION93.73
6.11-29.530.21221500.22912853X-RAY DIFFRACTION96.28

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