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- PDB-7l5c: Structure of copper bound MEMO1 -

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Basic information

Entry
Database: PDB / ID: 7l5c
TitleStructure of copper bound MEMO1
ComponentsProtein MEMO1
KeywordsMETAL BINDING PROTEIN / Breast Cancer / Metastasis / Cell motility / iron binding protein
Function / homologyMEMO1 family / Memo-like protein / regulation of microtubule-based process / ERBB2 Regulates Cell Motility / nucleus / cytosol / COPPER (I) ION / Protein MEMO1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 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_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

Downloads & links

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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)135,10625
Polymers133,7674
Non-polymers1,33921
Water2,216123
1
A: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6294
Polymers33,4421
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7225
Polymers33,4421
Non-polymers2804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,00210
Polymers33,4421
Non-polymers5609
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7546
Polymers33,4421
Non-polymers3125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.630, 87.160, 98.590
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 7 through 22 or (resid 23...
21(chain B and (resid 7 through 32 or (resid 33...
31(chain C and (resid 7 through 23 or (resid 24...
41(chain D and (resid 7 through 23 or (resid 24...

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-ID
11CYSCYSPROPRO(chain A and (resid 7 through 22 or (resid 23...AA7 - 224 - 19
12GLNGLNLEULEU(chain A and (resid 7 through 22 or (resid 23...AA23 - 2420 - 21
13VALVALHISHIS(chain A and (resid 7 through 22 or (resid 23...AA5 - 2972 - 294
14VALVALHISHIS(chain A and (resid 7 through 22 or (resid 23...AA5 - 2972 - 294
15VALVALHISHIS(chain A and (resid 7 through 22 or (resid 23...AA5 - 2972 - 294
16VALVALHISHIS(chain A and (resid 7 through 22 or (resid 23...AA5 - 2972 - 294
21CYSCYSLEULEU(chain B and (resid 7 through 32 or (resid 33...BB7 - 324 - 29
22SERSERSERSER(chain B and (resid 7 through 32 or (resid 33...BB3330
23VALVALHISHIS(chain B and (resid 7 through 32 or (resid 33...BB6 - 2973 - 294
24VALVALHISHIS(chain B and (resid 7 through 32 or (resid 33...BB6 - 2973 - 294
25VALVALHISHIS(chain B and (resid 7 through 32 or (resid 33...BB6 - 2973 - 294
26VALVALHISHIS(chain B and (resid 7 through 32 or (resid 33...BB6 - 2973 - 294
31CYSCYSGLNGLN(chain C and (resid 7 through 23 or (resid 24...CC7 - 234 - 20
32LEULEULEULEU(chain C and (resid 7 through 23 or (resid 24...CC2421
33VALVALHISHIS(chain C and (resid 7 through 23 or (resid 24...CC5 - 2972 - 294
34VALVALHISHIS(chain C and (resid 7 through 23 or (resid 24...CC5 - 2972 - 294
35VALVALHISHIS(chain C and (resid 7 through 23 or (resid 24...CC5 - 2972 - 294
36VALVALHISHIS(chain C and (resid 7 through 23 or (resid 24...CC5 - 2972 - 294
41CYSCYSGLNGLN(chain D and (resid 7 through 23 or (resid 24...DD7 - 234 - 20
42LEULEULEULEU(chain D and (resid 7 through 23 or (resid 24...DD2421
43VALVALVALVAL(chain D and (resid 7 through 23 or (resid 24...DD5 - 2962 - 293

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Components

#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 / Memo-1


Mass: 33441.770 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES pH 5.5-7.0 22% PEG3350 crystallization under anaerobic conditions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9801 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: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.55→42.91 Å / Num. obs: 40238 / % possible obs: 99.82 % / Redundancy: 14.854 % / Biso Wilson estimate: 39.053 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.193 / Χ2: 0.813 / Net I/σ(I): 16.56
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
2.55-2.6715.0291.0923.1376841511451130.8861.13100
2.67-2.815.0250.8144.269027459445940.9460.842100
2.8-2.9415.0330.6255.3860853404940480.960.647100
2.94-3.115.0280.4637.1357781384538450.9810.479100
3.1-3.2814.9880.31810.1951889346334620.9910.329100
3.28-3.4814.970.2271445673305130510.9940.235100
3.48-3.714.9380.16518.7939465264226420.9970.17100
3.7-3.9614.8660.12324.0336378244724470.9980.128100
3.96-4.2514.8630.09329.630544205520550.9990.097100
4.25-4.614.7870.07435.6427429185518550.9990.077100
4.6-514.7450.0736.3822472152415240.9990.073100
5-42.9114.1620.06338.0279337561556020.9990.06599.8

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KQ8

7kq8


Resolution: 2.55→42.91 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 3797 4.98 %
Rwork0.1891 72432 -
obs0.1919 40238 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.51 Å2 / Biso mean: 44.7183 Å2 / Biso min: 20.95 Å2
Refinement stepCycle: final / Resolution: 2.55→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9070 0 74 123 9267
Biso mean--53 39.72 -
Num. residues----1170
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3504X-RAY DIFFRACTION2.824TORSIONAL
12B3504X-RAY DIFFRACTION2.824TORSIONAL
13C3504X-RAY DIFFRACTION2.824TORSIONAL
14D3504X-RAY DIFFRACTION2.824TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.580.33651400.294626822822100
2.58-2.620.32131420.272226522794100
2.62-2.650.31411400.259727152855100
2.65-2.690.28641440.248126642808100
2.69-2.730.35351390.245826922831100
2.73-2.770.31791420.241126702812100
2.77-2.820.30221410.223927192860100
2.82-2.870.31171370.214826752812100
2.87-2.920.26221430.220127132856100
2.92-2.980.3041370.221426532790100
2.98-3.040.27611420.225226482790100
3.04-3.10.30061410.210627162857100
3.1-3.170.26761430.204426762819100
3.17-3.250.24381380.193126742812100
3.25-3.340.23851390.188126992838100
3.34-3.440.26771480.176326832831100
3.44-3.550.26451410.17726502791100
3.55-3.680.23641410.1827132854100
3.68-3.820.22031400.16626652805100
3.82-40.20091450.158626952840100
4-4.210.20561370.15626602797100
4.21-4.470.2371410.150627072848100
4.47-4.820.22621360.142526912827100
4.82-5.30.21861400.169826732813100
5.3-6.070.26191370.195726892826100
6.07-7.630.22681450.205426862831100
7.64-42.910.16171380.17482672281099
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)
12.05610.15290.36030.79330.17023.51370.0364-0.21780.00910.003-0.03510.0403-0.1306-0.2304-0.00170.2328-0.0039-0.00060.3125-0.01470.284919.831920.722711.423
21.32690.11081.39971.0702-1.09296.7839-0.02150.04320.1131-0.18790.00180.03120.5103-0.08770.06060.3318-0.0130.00860.3739-0.02480.306519.556714.76859.6046
31.6642-0.0907-1.08041.07460.42043.7073-0.00210.0805-0.13230.0265-0.085-0.0292-0.03890.02630.08020.2025-0.019-0.00950.29440.01870.257654.738424.51499.8547
41.25230.1721-0.39740.6525-0.24426.95150.0899-0.04450.00240.01740.1176-0.02920.62830.269-0.10990.29130.013-0.01710.30930.01290.303856.224118.433960.5569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 297)A5 - 297
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 297)B6 - 297
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 297)C5 - 297
4X-RAY DIFFRACTION4(chain 'D' and resid 5 through 297)D5 - 297

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