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- PDB-7m8h: Structure of Memo1 C244S metal binding site mutant at 1.75A -

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Basic information

Entry
Database: PDB / ID: 7m8h
TitleStructure of Memo1 C244S metal binding site mutant at 1.75A
ComponentsProtein MEMO1
KeywordsMETAL BINDING PROTEIN / Breast Cancer / iron binding protein
Function / homologyMEMO1 family / Memo-like protein / regulation of microtubule-based process / ERBB2 Regulates Cell Motility / nucleus / cytosol / GLUTATHIONE / DI(HYDROXYETHYL)ETHER / Protein MEMO1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBoniecki, M.T. / Uhlemann, E.E. / Dmitriev, O.Y.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06822 Canada
CitationJournal: Elife / Year: 2024
Title: MEMO1 binds iron and modulates iron homeostasis in cancer cells.
Authors: Dolgova, N. / Uhlemann, E.E. / Boniecki, M.T. / Vizeacoumar, F.S. / Ara, A. / Nouri, P. / Ralle, M. / Tonelli, M. / Abbas, S.A. / Patry, J. / Elhasasna, H. / Freywald, A. / Vizeacoumar, F.J. / Dmitriev, O.Y.
History
DepositionMar 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 22, 2024Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein MEMO1
B: Protein MEMO1
C: Protein MEMO1
D: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,09949
Polymers133,7034
Non-polymers4,39645
Water24,6451368
1
A: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,46911
Polymers33,4261
Non-polymers1,04310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,44613
Polymers33,4261
Non-polymers1,02012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,49013
Polymers33,4261
Non-polymers1,06412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,69412
Polymers33,4261
Non-polymers1,26811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.000, 89.520, 97.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 14 or resid 16...
21(chain B and (resid 4 through 14 or resid 16...
31(chain C and (resid 4 through 14 or resid 16...
41(chain D and (resid 4 through 14 or resid 16...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label alt-ID
11ARGARGGLYGLY(chain A and (resid 4 through 14 or resid 16...AA4 - 141 - 11
12TRPTRPTYRTYR(chain A and (resid 4 through 14 or resid 16...AA16 - 1713 - 14
13ALAALALEULEU(chain A and (resid 4 through 14 or resid 16...AA19 - 2816 - 25
14ARGARGGSHGSH(chain A and (resid 4 through 14 or resid 16...AA - E4 - 3011
15ARGARGGSHGSH(chain A and (resid 4 through 14 or resid 16...AA - E4 - 3011
16ARGARGGSHGSH(chain A and (resid 4 through 14 or resid 16...AA - E4 - 3011
17ARGARGGSHGSH(chain A and (resid 4 through 14 or resid 16...AA - E4 - 3011
18ARGARGGSHGSH(chain A and (resid 4 through 14 or resid 16...AA - E4 - 3011
21ARGARGGLYGLY(chain B and (resid 4 through 14 or resid 16...BB4 - 141 - 11
22TRPTRPTYRTYR(chain B and (resid 4 through 14 or resid 16...BB16 - 1713 - 14
23ALAALALEULEU(chain B and (resid 4 through 14 or resid 16...BB19 - 2816 - 25
24ARGARGGSHGSH(chain B and (resid 4 through 14 or resid 16...BB - O4 - 3011A
25ARGARGGSHGSH(chain B and (resid 4 through 14 or resid 16...BB - O4 - 3011A
26ARGARGGSHGSH(chain B and (resid 4 through 14 or resid 16...BB - O4 - 3011A
27ARGARGGSHGSH(chain B and (resid 4 through 14 or resid 16...BB - O4 - 3011A
31ARGARGGLYGLY(chain C and (resid 4 through 14 or resid 16...CC4 - 141 - 11
32TRPTRPTYRTYR(chain C and (resid 4 through 14 or resid 16...CC16 - 1713 - 14
33ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
34ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
35GLNGLNGLNGLN(chain C and (resid 4 through 14 or resid 16...CC3633
36ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
37ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
38ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
39ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
310ARGARGHISHIS(chain C and (resid 4 through 14 or resid 16...CC4 - 2971 - 294
41ARGARGGLYGLY(chain D and (resid 4 through 14 or resid 16...DD4 - 141 - 11
42TRPTRPTYRTYR(chain D and (resid 4 through 14 or resid 16...DD16 - 1713 - 14
43ALAALALEULEU(chain D and (resid 4 through 14 or resid 16...DD19 - 2816 - 25
44GLYGLYGLNGLN(chain D and (resid 4 through 14 or resid 16...DD30 - 3627 - 33
45PROPROGLYGLY(chain D and (resid 4 through 14 or resid 16...DD41 - 5638 - 53
46CYSCYSPROPRO(chain D and (resid 4 through 14 or resid 16...DD58 - 6855 - 65
47ILEILETHRTHR(chain D and (resid 4 through 14 or resid 16...DD70 - 7167 - 68
48ARGARGPROPRO(chain D and (resid 4 through 14 or resid 16...DD73 - 7970 - 76
49HISHISSERSER(chain D and (resid 4 through 14 or resid 16...DD81 - 9178 - 88
410ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
411ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
412ARGARGHISHIS(chain D and (resid 4 through 14 or resid 16...DD121 - 147118 - 144
413ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
414LYSLYSLYSLYS(chain D and (resid 4 through 14 or resid 16...DD148145
415ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
416ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
417ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
418ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
419ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011
420ARGARGGSHGSH(chain D and (resid 4 through 14 or resid 16...DD - MA4 - 3011

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein MEMO1 / C21orf19-like protein / Hepatitis C virus NS5A-transactivated protein 7 / HCV NS5A-transactivated ...C21orf19-like protein / Hepatitis C virus NS5A-transactivated protein 7 / HCV NS5A-transactivated protein 7 / Mediator of ErbB2-driven cell motility 1 / Mediator of cell motility 1 / Memo-1


Mass: 33425.707 Da / Num. of mol.: 4 / Mutation: C244S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEMO1, C2orf4, MEMO, NS5ATP7, CGI-27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y316

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Non-polymers , 6 types, 1413 molecules

#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1368 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 46.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES pH 5.5-7.0 22 % PEG3350 under anaerobic conditions
PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.968 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.75→42.63 Å / Num. obs: 238611 / % possible obs: 99.9 % / Redundancy: 14.819 % / Biso Wilson estimate: 18.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.091 / Χ2: 0.889 / Net I/σ(I): 27.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.8614.2721.0523.229151420470204260.8931.09199.8
1.86-1.9814.920.4767.0626050517482174600.9750.49299.9
1.98-2.1214.9630.25112.6523499215714157050.9910.25999.9
2.12-2.2814.9990.1519.8220396313602135980.9960.155100
2.28-2.4715.0230.10826.4417891811910119100.9980.111100
2.47-2.715.0270.08433.0615533510337103370.9990.087100
2.7-2.9715.0140.06641.05126011839383930.9990.068100
2.97-3.314.9720.0551.44103638692269220.9990.052100
3.3-3.7214.9610.03566.39843215636563610.036100
3.72-4.2714.8950.02877.71667614482448210.029100
4.27-514.7950.02585.91484683276327610.026100
5-42.6314.1690.02675.54801095669565410.02799.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KQ8

7kq8


Resolution: 1.75→42.63 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1872 11932 5 %
Rwork0.154 226679 -
obs0.1556 238611 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.64 Å2 / Biso mean: 22.5935 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 1.75→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9358 0 323 1368 11049
Biso mean--41.91 33.36 -
Num. residues----1176
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4920X-RAY DIFFRACTION9.299TORSIONAL
12B4920X-RAY DIFFRACTION9.299TORSIONAL
13C4920X-RAY DIFFRACTION9.299TORSIONAL
14D4920X-RAY DIFFRACTION9.299TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.33773930.308975237916100
1.77-1.790.29263970.255375647961100
1.79-1.810.2843960.230974877883100
1.81-1.840.27714010.23376068007100
1.84-1.860.34643960.271375437939100
1.86-1.890.30323910.280275307921100
1.89-1.910.24743930.229775757968100
1.91-1.940.23143970.196275557952100
1.94-1.970.22744020.172375417943100
1.97-20.20214000.158776158015100
2-2.040.19433960.154375457941100
2.04-2.070.21463940.158475617955100
2.07-2.110.18873930.155675017894100
2.11-2.160.19274010.15475897990100
2.16-2.20.18733990.150475397938100
2.2-2.260.16854000.146575657965100
2.26-2.310.16594000.134975697969100
2.31-2.370.19594060.142575978003100
2.37-2.440.19773970.145575507947100
2.44-2.520.20713950.151675647959100
2.52-2.610.21233950.146875577952100
2.61-2.720.18673990.148276048003100
2.72-2.840.19913980.147675267924100
2.84-2.990.17363980.145575507948100
2.99-3.180.16993960.141275607956100
3.18-3.420.17024050.142575757980100
3.42-3.770.15733940.127875747968100
3.77-4.310.14864010.120175297930100
4.31-5.430.12613960.123475827978100
5.43-42.630.17684030.16917503790699
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)
10.67170.12580.24330.5205-0.02781.03140.00770.0503-0.012-0.03820.0324-0.0101-0.03010.0162-0.0420.1112-0.00170.01070.0873-0.00230.104718.128723.827811.7495
20.7575-0.07210.19030.3621-0.00141.3048-0.0230.02980.0624-0.0127-0.0467-0.054-0.00580.04240.06570.10740.00670.01320.08560.03160.1383-16.668422.708336.7823
30.66860.20430.20620.2371-0.07730.7365-0.01370.02690.0445-0.00070.0127-0.0022-0.0321-0.00970.01350.11450.0075-0.00990.09540.00390.09418.10516.821357.803
40.7491-0.13380.63930.2081-0.09551.2335-0.0655-0.0110.07050.0307-0.0467-0.0485-0.0570.09110.09370.125-0.0104-0.02020.10160.02150.1478-16.531417.9917-9.3567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 301)A4 - 301
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 301)B4 - 301
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 301)C4 - 301
4X-RAY DIFFRACTION4(chain 'D' and resid 4 through 301)D4 - 301

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