PDB-5cmb: Mnemiopsis leidyi ML032222a iGluR LBD R703K mutant glycine complex

ID or keywords:

Entry

Database: PDB / ID: 5cmb

Title

Mnemiopsis leidyi ML032222a iGluR LBD R703K mutant glycine complex

Components

ML032222a iGluR

Keywords

MEMBRANE PROTEIN / Glutamate Receptor / Ion Channel

Function / homology

Function and homology information

ligand-gated monoatomic ion channel activity / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Mnemiopsis leidyi (sea walnut)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.34 Å

Authors

Mayer, M.L. / Thomas, A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Molecular lock regulates binding of glycine to a primitive NMDA receptor.
Authors: Yu, A. / Alberstein, R. / Thomas, A. / Zimmet, A. / Grey, R. / Mayer, M.L. / Lau, A.Y.

History

Deposition	Jul 16, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Nov 16, 2016	Group: Database references
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5cmb.cif.gz	313.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5cmb.ent.gz	259.6 KB	Display	PDB format
PDBx/mmJSON format	5cmb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5cmb_validation.pdf.gz	462.6 KB	Display	wwPDB validaton report
Full document	5cmb_full_validation.pdf.gz	465.4 KB	Display
Data in XML	5cmb_validation.xml.gz	27.9 KB	Display
Data in CIF	5cmb_validation.cif.gz	44 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cm/5cmb ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cmb	HTTPS FTP

-
Related structure data

Related structure data	5cmcC 4ykiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ykp-d 4ykk-d 4yki-d 3ijx-1 4ykj-d 2ylz-d 5ybg-1 2isq-1 4bdn-2 5elv-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (6) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: ML032222a iGluR

B: ML032222a iGluR

hetero molecules

58.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	45.731, 123.389, 54.334
Angle α, β, γ (deg.)	90.00, 112.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ML032222a iGluR Mass: 28933.547 Da / Num. of mol.: 2 / Mutation: R681K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mnemiopsis leidyi (sea walnut) / Gene: ML032222a / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: A0A0R4I973*PLUS
#2: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.24 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: Reservoir: 24% PEG 8K, 100 mM Cacodylate, 150 mM MgS04. Protein buffer: 150 mM NaCl, 10 mM HEPES, pH 7.0, 0.5 mM EDTA, 10 mM glycine PH range: 6.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.34→40 Å / Num. obs: 124741 / % possible obs: 97.8 % / Redundancy: 4.4 % / R_merge(I) obs: 0.045 / Net I/σ(I): 31.1
Reflection shell	Resolution: 1.34→1.36 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.365 / Mean I/σ(I) obs: 2.4 / % possible all: 72.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4YKI

4yki

Resolution: 1.34→38.988 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1667	6166	5.06 %	Random selection
R_work	0.1432	-	-	-
obs	0.1444	121955	97.77 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.34→38.988 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4002	0	16	780	4798

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4226
X-RAY DIFFRACTION	f_angle_d	1.239	5716
X-RAY DIFFRACTION	f_dihedral_angle_d	12.878	1556
X-RAY DIFFRACTION	f_chiral_restr	0.068	609
X-RAY DIFFRACTION	f_plane_restr	0.006	748

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.3393-1.3545	0.2313	149	0.2183	2710	X-RAY DIFFRACTION	69
1.3545-1.3705	0.2556	182	0.2153	3134	X-RAY DIFFRACTION	80
1.3705-1.3872	0.2299	185	0.2159	3508	X-RAY DIFFRACTION	89
1.3872-1.4047	0.2385	190	0.2017	3784	X-RAY DIFFRACTION	96
1.4047-1.4232	0.2037	219	0.1771	3902	X-RAY DIFFRACTION	100
1.4232-1.4427	0.1758	199	0.1764	3965	X-RAY DIFFRACTION	100
1.4427-1.4633	0.1818	206	0.1671	3961	X-RAY DIFFRACTION	100
1.4633-1.4852	0.1868	210	0.1596	3912	X-RAY DIFFRACTION	100
1.4852-1.5084	0.1842	212	0.1571	3909	X-RAY DIFFRACTION	100
1.5084-1.5331	0.181	205	0.1522	3964	X-RAY DIFFRACTION	100
1.5331-1.5595	0.1861	214	0.1493	3952	X-RAY DIFFRACTION	100
1.5595-1.5879	0.1844	218	0.1496	3930	X-RAY DIFFRACTION	100
1.5879-1.6184	0.1717	199	0.1438	3940	X-RAY DIFFRACTION	100
1.6184-1.6515	0.192	216	0.1438	3946	X-RAY DIFFRACTION	100
1.6515-1.6874	0.1802	209	0.147	3953	X-RAY DIFFRACTION	100
1.6874-1.7266	0.1646	207	0.1447	3914	X-RAY DIFFRACTION	100
1.7266-1.7698	0.1712	209	0.1422	3990	X-RAY DIFFRACTION	100
1.7698-1.8177	0.1535	216	0.1371	3927	X-RAY DIFFRACTION	100
1.8177-1.8712	0.1581	203	0.143	3940	X-RAY DIFFRACTION	100
1.8712-1.9316	0.1599	217	0.1445	3956	X-RAY DIFFRACTION	100
1.9316-2.0006	0.169	207	0.142	3919	X-RAY DIFFRACTION	100
2.0006-2.0807	0.1515	202	0.1355	4002	X-RAY DIFFRACTION	100
2.0807-2.1754	0.1566	201	0.1338	3957	X-RAY DIFFRACTION	100
2.1754-2.29	0.1539	204	0.1336	3943	X-RAY DIFFRACTION	100
2.29-2.4335	0.163	195	0.1362	3953	X-RAY DIFFRACTION	100
2.4335-2.6214	0.1837	190	0.141	3972	X-RAY DIFFRACTION	100
2.6214-2.8851	0.1528	222	0.1437	3962	X-RAY DIFFRACTION	100
2.8851-3.3024	0.1541	202	0.1407	3966	X-RAY DIFFRACTION	100
3.3024-4.1599	0.1565	220	0.1232	3980	X-RAY DIFFRACTION	100
4.1599-39.0048	0.1597	258	0.1403	3938	X-RAY DIFFRACTION	100

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	0.301	-0.0469	0.0187	0.0985	0.0001	0.1635	0.0071	-0.0215	-0.0659	-0.0309	-0.0309	-0.0168	0.0567	0.078	0.0002	0.1148	0.0182	-0.0032	0.0884	0.0055	0.1439	21.49	54.4283	49.7984
2	0.0788	-0.1437	0.1264	0.3285	-0.0789	0.4247	-0.0009	-0.0436	-0.0406	0.0149	-0.0056	0.0318	0.068	-0.0151	-0	0.103	-0.0013	-0.0159	0.0838	-0.0027	0.1673	12.5411	57.4647	54.4017
3	0.7456	-0.0364	-0.0891	0.2002	0.0974	0.3107	-0.0232	0.0933	-0.0083	-0.0491	-0.0057	0.013	-0.0087	-0.0563	0.0018	0.1058	-0.0137	-0.0083	0.0918	-0.0075	0.1301	3.6548	61.5562	42.7634
4	0.8387	0.2004	0.174	0.1426	-0.123	0.5434	-0.0927	0.1954	-0.0006	-0.0539	0.0429	0.0555	0.0314	0.0392	-0.009	0.0981	-0.0056	-0.0085	0.105	-0.0269	0.139	2.6076	59.6191	36.8872
5	0.2794	-0.0331	-0.0216	0.1001	-0.089	0.0816	-0.0183	0.0466	0.0341	-0.02	-0.018	-0.0433	-0.0181	-0.0286	-0	0.1094	-0.0098	-0.0018	0.1012	0.0053	0.1279	23.0286	68.8714	47.1636
6	0.6472	-0.0153	0.0497	0.2282	0.2696	0.3554	0.0258	0.0056	-0.0128	0.0215	-0.0148	0.02	-0.048	-0.083	0.0048	0.0942	0.0138	0.0044	0.0764	0.0039	0.0685	5.6656	94.8085	49.3467
7	0.2231	-0.2059	-0.1158	0.4029	0.2306	0.5869	0.0161	-0.0832	0.0145	0.0095	0.0066	-0.0229	-0.0319	0.0313	0.0067	0.0706	-0.0049	0.0015	0.0711	0.0004	0.0648	15.6616	93.1849	54.0833
8	0.6905	0.097	-0.5989	-0.0241	-0.1546	1.012	-0.0165	0.0825	-0.0784	-0.0169	-0.0031	-0.0244	0.0029	-0.0174	0.0229	0.0807	-0.0034	0.0053	0.0785	-0.0056	0.0629	25.1187	88.3308	36.0162
9	0.2021	-0.075	-0.0788	0.0102	0.0469	0.0486	-0.0485	0.0091	-0.0368	-0.0017	-0.0391	-0.0023	0.0149	-0.0032	-0	0.1032	-0.0042	0.0014	0.1043	-0.0128	0.1292	4.3155	79.4123	50.371
10	0.1017	-0.1976	-0.1248	0.3245	0.2172	0.1627	-0.1725	0.5739	-0.0275	-0.0054	-0.0425	-0.0333	0.0159	0.2523	-0.0281	0.116	-0.0268	-0.0194	0.3136	0.011	0.1067	5.6798	89.2804	29.0969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:43)
2	X-RAY DIFFRACTION	2	(chain A and resid 44:72)
3	X-RAY DIFFRACTION	3	(chain A and resid 73:143)
4	X-RAY DIFFRACTION	4	(chain A and resid 144:220)
5	X-RAY DIFFRACTION	5	(chain A and resid 221:251)
6	X-RAY DIFFRACTION	6	(chain B and resid 1:43)
7	X-RAY DIFFRACTION	7	(chain B and resid 44:89)
8	X-RAY DIFFRACTION	8	(chain B and resid 90:220)
9	X-RAY DIFFRACTION	9	(chain B and resid 221:244)
10	X-RAY DIFFRACTION	10	(chain B and resid 245:255)

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi