PDB-7kq8: Structure of iron bound MEMO1

ID or keywords:

Entry

Database: PDB / ID: 7kq8

Title

Structure of iron bound MEMO1

Components

Protein MEMO1

Keywords

METAL BINDING PROTEIN / Breast Cancer / Metastasis / Cell motility / iron binding protein

Function / homology

Function and homology information

regulation of microtubule-based process / ERBB2 Regulates Cell Motility / nucleus / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Boniecki, M.T. / Uhlemann, E.E. / Dmitriev, O.Y.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	Nov 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	May 22, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kq8.cif.gz	487.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7kq8.ent.gz	401.4 KB	Display	PDB format
PDBx/mmJSON format	7kq8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7kq8_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	7kq8_full_validation.pdf.gz	3.8 MB	Display
Data in XML	7kq8_validation.xml.gz	51.2 KB	Display
Data in CIF	7kq8_validation.cif.gz	72.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/7kq8 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/7kq8	HTTPS FTP

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Related structure data

Related structure data	7l5cC 7m8hC 3bczS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7kq8-3 4l20-d 7kq8-2 3bcz-3 3r43-d 5tc6-d 3mmr-d 3bd0-3 6dno-d 6qpp-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7l5cC

7m8hC

3bczS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #212 - Aug 2017 Glutathione Transferases similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#126 - Jun 2010
Epidermal Growth Factor
similarity (1)
#212 - Aug 2017
Glutathione Transferases
similarity (1)
#111 - Mar 2009
Hydrogenase
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (1)
#61 - Jan 2005
Phenylalanine Hydroxylase
similarity (1)

Deposited unit

A: Protein MEMO1

B: Protein MEMO1

C: Protein MEMO1

D: Protein MEMO1

hetero molecules

138 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein MEMO1

hetero molecules

defined by author&software
Evidence: gel filtration
34.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein MEMO1

hetero molecules

defined by author&software
34.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Protein MEMO1

hetero molecules

defined by author&software
34.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Protein MEMO1

hetero molecules

defined by author&software
34.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	139.643, 88.861, 97.360
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and ((resid 4 and (name N or name...
2	1	(chain B and (resid 4 through 14 or resid 16...
3	1	(chain C and (resid 4 through 5 or (resid 6...
4	1	(chain D and ((resid 4 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	ARG	ARG	(chain A and ((resid 4 and (name N or name...	A	A	4	1
1	2	ARG	ARG	GSH	GSH	(chain A and ((resid 4 and (name N or name...	A	A - E	4 - 301	1
1	3	ARG	ARG	GSH	GSH	(chain A and ((resid 4 and (name N or name...	A	A - E	4 - 301	1
1	4	ARG	ARG	GSH	GSH	(chain A and ((resid 4 and (name N or name...	A	A - E	4 - 301	1
1	5	ARG	ARG	GSH	GSH	(chain A and ((resid 4 and (name N or name...	A	A - E	4 - 301	1
2	1	ARG	ARG	GLY	GLY	(chain B and (resid 4 through 14 or resid 16...	B	B	4 - 14	1 - 11
2	2	TRP	TRP	PRO	PRO	(chain B and (resid 4 through 14 or resid 16...	B	B	16 - 22	13 - 19
2	3	LEU	LEU	LEU	LEU	(chain B and (resid 4 through 14 or resid 16...	B	B	24 - 28	21 - 25
2	4	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
2	5	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
2	6	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
2	7	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
2	8	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
2	9	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
2	10	ARG	ARG	GSH	GSH	(chain B and (resid 4 through 14 or resid 16...	B	B - V	4 - 301	1
3	1	ARG	ARG	VAL	VAL	(chain C and (resid 4 through 5 or (resid 6...	C	C	4 - 5	1 - 2
3	2	VAL	VAL	VAL	VAL	(chain C and (resid 4 through 5 or (resid 6...	C	C	6	3
3	3	ARG	ARG	HIS	HIS	(chain C and (resid 4 through 5 or (resid 6...	C	C	4 - 297	1 - 294
3	4	ARG	ARG	HIS	HIS	(chain C and (resid 4 through 5 or (resid 6...	C	C	4 - 297	1 - 294
3	5	ARG	ARG	HIS	HIS	(chain C and (resid 4 through 5 or (resid 6...	C	C	4 - 297	1 - 294
4	1	ARG	ARG	ARG	ARG	(chain D and ((resid 4 and (name N or name...	D	D	4	1
4	2	ARG	ARG	HIS	HIS	(chain D and ((resid 4 and (name N or name...	D	D	4 - 297	1 - 294
4	3	ARG	ARG	HIS	HIS	(chain D and ((resid 4 and (name N or name...	D	D	4 - 297	1 - 294
4	4	ARG	ARG	HIS	HIS	(chain D and ((resid 4 and (name N or name...	D	D	4 - 297	1 - 294
4	5	ARG	ARG	HIS	HIS	(chain D and ((resid 4 and (name N or name...	D	D	4 - 297	1 - 294

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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 / 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

#1: Protein

Protein MEMO1 / C21orf19-like protein / Hepatitis C virus NS5A-transactivated protein 7 / HCV NS5A-transactivated ...

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

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Non-polymers , 6 types, 653 molecules

#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.52 %
Crystal grow	Temperature: 301 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 5.5-7.0 22% PEG3350 crystallization under anaerobic conditions PH range: 5.5-7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.978 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 2.15→48.68 Å / Num. obs: 127620 / % possible obs: 99.9 % / Redundancy: 6.909 % / B_iso Wilson estimate: 28.363 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.132 / R_rim(I) all: 0.143 / Χ²: 1.094 / Net I/σ(I): 13.6 / Num. measured all: 881674 / Scaling rejects: 22

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.15-2.2	6.499	0.513	4.24	61029	9457	9391	0.923	0.558	99.3
2.2-2.26	6.886	0.433	5.29	63829	9273	9270	0.952	0.469	100
2.26-2.33	6.676	0.37	6.2	59782	8961	8955	0.964	0.401	99.9
2.33-2.4	6.986	0.359	6.79	60890	8717	8716	0.967	0.388	100
2.4-2.48	6.741	0.348	7.15	56280	8352	8349	0.967	0.377	100
2.48-2.57	7.15	0.334	8.29	58380	8165	8165	0.974	0.36	100
2.57-2.66	7.072	0.277	9.48	55750	7885	7883	0.98	0.299	100
2.66-2.77	6.802	0.248	10.33	51381	7556	7554	0.983	0.268	100
2.77-2.9	7.073	0.215	11.87	51451	7275	7274	0.985	0.232	100
2.9-3.04	6.879	0.166	13.92	47653	6927	6927	0.991	0.179	100
3.04-3.2	7.062	0.139	15.99	46635	6605	6604	0.994	0.15	100
3.2-3.4	7.083	0.109	19.31	44103	6227	6227	0.995	0.118	100
3.4-3.63	6.809	0.088	22.08	39992	5873	5873	0.996	0.095	100
3.63-3.92	7.074	0.076	25.07	38474	5439	5439	0.997	0.082	100
3.92-4.3	6.884	0.067	26.94	34579	5023	5023	0.997	0.072	100
4.3-4.8	7.081	0.059	29.46	32339	4568	4567	0.998	0.064	100
4.8-5.55	6.92	0.063	26.61	27583	3986	3986	0.998	0.068	100
5.55-6.79	6.943	0.068	24.81	23424	3374	3374	0.998	0.073	100
6.79-9.61	6.955	0.054	28.12	18242	2623	2623	0.998	0.059	100
9.61-48.68	6.956	0.049	30.77	9878	1431	1420	0.998	0.053	99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc3_4028	refinement
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BCZ

3bcz

Resolution: 2.15→48.68 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.202	3810	2.99 %
R_work	0.1592	123745	-
obs	0.1604	127555	99.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 82.44 Å² / B_iso mean: 26.4591 Å² / B_iso min: 12.28 Å²

Refinement step

Cycle: final / Resolution: 2.15→48.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9275	0	351	597	10223
B_iso mean	-	-	37.46	32.52	-
Num. residues	-	-	-	-	1176

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	5156	X-RAY DIFFRACTION	10.171	TORSIONAL
1	2	B	5156	X-RAY DIFFRACTION	10.171	TORSIONAL
1	3	C	5156	X-RAY DIFFRACTION	10.171	TORSIONAL
1	4	D	5156	X-RAY DIFFRACTION	10.171	TORSIONAL

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.15-2.17	0.2674	139	0.216	4529	4668	98
2.17-2.2	0.2394	142	0.2031	4557	4699	100
2.2-2.23	0.2345	145	0.1938	4598	4743	100
2.23-2.27	0.2997	140	0.1931	4583	4723	100
2.27-2.3	0.2352	142	0.1792	4612	4754	100
2.3-2.34	0.2742	141	0.1836	4560	4701	100
2.34-2.37	0.2304	142	0.1825	4589	4731	100
2.37-2.41	0.2297	142	0.1811	4591	4733	100
2.41-2.46	0.2359	134	0.1832	4588	4722	100
2.46-2.51	0.2081	143	0.1824	4604	4747	100
2.51-2.56	0.2273	143	0.1745	4575	4718	100
2.56-2.61	0.2615	143	0.1768	4580	4723	100
2.61-2.67	0.2523	141	0.1613	4568	4709	100
2.67-2.74	0.213	142	0.1721	4582	4724	100
2.74-2.81	0.2919	143	0.17	4603	4746	100
2.81-2.9	0.2264	146	0.1722	4584	4730	100
2.9-2.99	0.1981	138	0.169	4568	4706	100
2.99-3.1	0.1843	140	0.1702	4573	4713	100
3.1-3.22	0.2156	139	0.1611	4603	4742	100
3.22-3.37	0.1841	146	0.1489	4611	4757	100
3.37-3.55	0.1991	141	0.1422	4583	4724	100
3.55-3.77	0.1882	140	0.1347	4610	4750	100
3.77-4.06	0.1684	139	0.1279	4585	4724	100
4.06-4.47	0.1412	142	0.1211	4577	4719	100
4.47-5.11	0.1288	144	0.1251	4595	4739	100
5.11-6.44	0.1984	130	0.1719	4577	4707	100
6.44-48.68	0.1788	143	0.1697	4560	4703	99

Refinement TLS params.

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

ID	L11 (°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)
1	0.8135	0.061	0.2705	0.6484	-0.0704	2.3872	0.036	0.0384	-0.0398	-0.0372	0.0431	-0.0223	0.0091	-0.0501	-0.0658	0.1159	-0.0049	0.0043	0.0895	-0.0026	0.1651	18.0385	23.8715	11.714
2	0.7719	-0.1054	0.1338	0.4745	-0.1579	2.224	-0.0321	0.0007	0.0251	-0.0475	-0.0627	-0.0595	0.0031	0.0594	0.0826	0.1305	0.0008	0.0149	0.0875	0.0286	0.1995	-16.4412	22.5126	36.8309
3	1.1945	-0.0746	0.5198	0.5575	0.0344	2.4223	-0.0528	-0.0153	0.076	0.0515	-0.0871	-0.0716	-0.0286	0.1685	0.1166	0.1448	0.0007	-0.0181	0.1357	0.028	0.1989	-16.8994	18.0201	-9.7296
4	1.1615	0.0794	0.0684	0.7917	-0.1482	2.1414	-0.0034	0.0264	0.0504	0.0164	0.0071	-0.0104	-0.0012	0.0464	-0.0009	0.1146	0.0157	-0.014	0.096	-0.0047	0.1473	18.4964	17.044	58.5989

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 4 through 297)	A	4 - 297
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 4 through 297)	B	4 - 297
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 4 through 297)	C	4 - 297
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 4 through 297)	D	4 - 297

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 653 molecules

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 653 molecules

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Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi