PDB-7rw5: Crystal structure of human methionine adenosyltransferase 2A (MAT...

ID or keywords:

Entry

Database: PDB / ID: 7rw5

Title

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor Compound 1

Components

S-adenosylmethionine synthase isoform type-2

Keywords

TRANSFERASE/INHIBITOR /

METHIONINE ADENOSYLTRANSFERASE / SAM / ALLOSTERIC INHIBITOR /

TRANSFERASE / TRANSFERASE-INHIBITOR COMPLEX

Function / homology

Function and homology information

methionine adenosyltransferase complex /

methionine adenosyltransferase /

methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process /

Methylation / protein heterooligomerization / protein hexamerization /

small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Jin, L. / Padyana, A.K.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads.
Authors: Li, M. / Konteatis, Z. / Nagaraja, N. / Chen, Y. / Zhou, S. / Ma, G. / Gross, S. / Marjon, K. / Hyer, M.L. / Mandley, E. / Lein, M. / Padyana, A.K. / Jin, L. / Tong, S. / Peters, R. / ...

History

Deposition	Aug 19, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2022	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Apr 6, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7rw5.cif.gz	707 KB	Display	PDBx/mmCIF format
PDB format	pdb7rw5.ent.gz	485.9 KB	Display	PDB format
PDBx/mmJSON format	7rw5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rw/7rw5 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rw5	HTTPS FTP

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Related structure data

Related structure data	7rw7C 7rwgC 7rwhC 2p02S 7kcc S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: S-adenosylmethionine synthase isoform type-2

B: S-adenosylmethionine synthase isoform type-2

C: S-adenosylmethionine synthase isoform type-2

D: S-adenosylmethionine synthase isoform type-2

hetero molecules

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

1

A: S-adenosylmethionine synthase isoform type-2

B: S-adenosylmethionine synthase isoform type-2

hetero molecules

defined by author
Evidence: gel filtration
88.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: S-adenosylmethionine synthase isoform type-2

D: S-adenosylmethionine synthase isoform type-2

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.237, 103.990, 113.972
Angle α, β, γ (deg.)	90.000, 93.473, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II Mass: 43807.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31153, methionine adenosyltransferase
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Chemical	ChemComp-7U2 / (3'R)-N-(cyclopropylmethyl)-1'-[(2-fluorophenyl)methyl]-4-methyl-5H,7H-spiro[pyrano[4,3-d]pyrimidine-8,3'-pyrrolidin]-2-amine Mass: 382.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₂₇FN₄O / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H₂O
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: 2.39 Å³/Da / Density % sol: 48.54 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M LiCl, 0.1 M Tris pH 8.0, (18%-20%) PEG6000, 10% Ethylene Glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.47→50 Å / Num. obs: 56196 / % possible obs: 99.4 % / Redundancy: 3.4 % / B_iso Wilson estimate: 37.06 Å² / R_merge(I) obs: 0.068 / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.47→2.56 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.535 / Mean I/σ(I) obs: 2 / Num. unique obs: 5514 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2P02

2p02

Resolution: 2.48→37.92 Å / SU ML: 0.2818 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2292	2752	5.05 %
R_work	0.1752	51776	-
obs	0.1779	54528	96.29 %

Solvent computation

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

Displacement parameters

B_iso mean: 45.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.48→37.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11435	0	82	459	11976

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0019	11760
X-RAY DIFFRACTION	f_angle_d	0.5006	15922
X-RAY DIFFRACTION	f_chiral_restr	0.0437	1772
X-RAY DIFFRACTION	f_plane_restr	0.003	2049
X-RAY DIFFRACTION	f_dihedral_angle_d	19.5305	4377

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 (%)
2.48-2.52	0.3001	92	0.243	1933	X-RAY DIFFRACTION	71.61
2.52-2.56	0.3114	127	0.237	2099	X-RAY DIFFRACTION	80.48
2.56-2.61	0.3145	140	0.2243	2432	X-RAY DIFFRACTION	90.37
2.61-2.67	0.3311	149	0.2122	2610	X-RAY DIFFRACTION	98.05
2.67-2.73	0.2644	130	0.2093	2695	X-RAY DIFFRACTION	99.12
2.73-2.79	0.2427	142	0.1943	2605	X-RAY DIFFRACTION	99.21
2.79-2.86	0.2707	124	0.1981	2722	X-RAY DIFFRACTION	99.37
2.86-2.94	0.2497	132	0.1973	2632	X-RAY DIFFRACTION	99.5
2.94-3.02	0.2757	117	0.1996	2723	X-RAY DIFFRACTION	99.61
3.02-3.12	0.273	139	0.1924	2662	X-RAY DIFFRACTION	99.12
3.12-3.23	0.2299	134	0.1763	2643	X-RAY DIFFRACTION	99.04
3.23-3.36	0.225	143	0.1717	2701	X-RAY DIFFRACTION	99.58
3.36-3.51	0.2101	158	0.163	2647	X-RAY DIFFRACTION	99.72
3.51-3.7	0.2013	144	0.1617	2682	X-RAY DIFFRACTION	99.79
3.7-3.93	0.2196	145	0.1536	2646	X-RAY DIFFRACTION	99.5
3.93-4.23	0.2057	148	0.1571	2656	X-RAY DIFFRACTION	98.42
4.23-4.66	0.1911	144	0.1452	2691	X-RAY DIFFRACTION	99.65
4.66-5.33	0.2072	150	0.1487	2688	X-RAY DIFFRACTION	99.06
5.33-6.71	0.2227	138	0.1852	2663	X-RAY DIFFRACTION	98.04
6.71-37.92	0.2175	156	0.1794	2646	X-RAY DIFFRACTION	96.29

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	1.08463959974	0.251963757357	0.597571442386	1.17925526641	0.636788301681	2.59380935968	-0.173101152392	-0.0209550512847	0.0624007864981	-0.0853618361279	0.105701383174	-0.152597283807	-0.447483199127	0.0947639600252	0.0232640868426	0.178891694547	-0.0237476095971	-0.0227370818996	0.167896122578	0.0259722615775	0.280086728119	16.0491441953	8.93504947782	9.72464789518
2	0.755552257595	-0.474121276819	-0.524311884933	1.53773332866	0.234468632456	3.26896329402	-0.0511997736082	-0.326428639395	0.0515172620235	0.0955187023537	0.0202137730139	-0.318816928266	-0.164759569931	0.484647830588	-0.0285267251539	0.246855036466	-0.0519093385074	-0.0577757324138	0.211574211001	-0.0170500291867	0.318454203303	19.6111345597	11.1618424282	15.746565608
3	2.50249553309	-0.18840218519	-0.345923607949	0.980200032065	0.413716791957	1.55863804032	-0.0519694921958	0.284423469421	-0.0111033107533	-0.114791109767	-0.0321852251005	0.144729319098	-0.0723713999293	-0.253556617708	0.0954490250112	0.209990537999	-0.0260780930436	-0.028245519329	0.246375565784	0.0385817628945	0.272000191357	1.62386716075	5.83528320343	-2.61588116582
4	2.33182385944	-0.524277653195	0.406596779933	1.45663272804	-0.0942693605613	2.04816488421	-0.0132079711842	0.636623943978	0.147808582114	-0.217207034702	-0.0675450414317	-0.249036736745	-0.229728318618	0.359232285789	0.0497357313413	0.262252939838	-0.100763391935	0.0495885682697	0.38566075589	0.0758574116224	0.347891628127	26.9463363235	9.18828186701	-13.1791669809
5	2.01716662177	-0.195511412179	-0.508796671436	1.37690728303	0.0411682181086	2.37471640117	-0.0879461475205	0.294384945375	0.386369571254	-0.258914689605	0.0236137276652	-0.0727279234655	-0.356662467632	-0.000636193421556	0.0435195435302	0.372856606362	-0.0576502532882	-0.0248721223566	0.219303712661	0.0810775488854	0.33306930167	18.587626045	17.4539614328	-4.48557970456
6	0.633638666183	-0.295800423894	0.585474881023	0.420245644237	0.352275322351	1.93663339119	0.0116850464508	-0.174706166759	-0.157177986962	0.044809602015	-0.0671465937692	0.0169473422434	0.258533678353	0.0130166797895	0.0648876389204	0.233420926759	-0.0425059310018	-0.00773545163397	0.159658857511	0.0324036098695	0.27810945541	21.9657463772	-11.7155578902	13.2705187234
7	0.19980543946	0.257921776927	0.900539577002	1.47264525247	1.05401591287	4.01646289308	-0.145807065845	0.0105197917278	0.0646592035563	-0.165346334179	-0.123888041182	0.754417638911	0.250835927246	-0.461535578541	0.220356171134	0.511050959939	-0.111701961826	0.0148378835718	0.387462066958	0.0040056703594	0.56141795769	4.24390790227	-11.806786751	14.3572258274
8	3.180122619	0.481515583973	0.915271307275	1.71112967019	-0.181253412492	2.45980935917	-0.0738216394121	0.192197132102	-0.225426336148	-0.245492469271	0.0455229202653	-0.233510330549	0.431818682125	0.251736402157	0.0398026412044	0.241312960861	0.00994215464104	0.0837699230878	0.188364033349	-0.00995325874526	0.306910455809	31.0747539577	-13.6045245914	-2.4575654704
9	1.99824938352	0.480530878843	-0.0788423612911	1.12279188643	-0.0280779261758	1.56322043904	-0.0250755717185	0.0672430919784	-0.0951070809862	-0.0897544137633	-0.000214390891658	-0.231810997434	0.0383620572643	0.283240285172	0.0258394088731	0.220544452155	0.00166951342215	0.0530539711591	0.206193183052	0.0177536373236	0.334388068986	33.8352885338	-8.40145403975	0.554113842339
10	2.70280630963	0.211109123737	0.435639260422	2.28161988272	-1.12507639427	2.14067675398	-0.123370240904	0.335782810851	-0.0287209243621	-0.247271242809	0.079379634898	0.0999679522135	0.0352005718998	-0.257857040283	0.0827373172957	0.32661581375	-0.0759281832327	-0.0226181760492	0.262663988376	-0.0516718401208	0.363081287243	10.3724403263	-16.0928029995	-12.1596652737
11	2.17429554219	0.15474703659	0.555227418811	1.89854450046	0.756898744816	3.37527251855	-0.0512586551687	0.287450432337	-0.263193901657	-0.153384493984	-0.057664911804	0.246584955089	0.349196460195	-0.247399453706	0.0432347384158	0.336244839186	-0.0611055849677	0.00790464171956	0.210966957594	-0.04651604752	0.343249765961	11.3643393176	-22.7288446035	-4.92090533174
12	1.41799071537	-0.423134282667	-0.0733539843997	1.27722651979	0.24320244884	1.27171237175	0.0356440586595	-0.0536741116919	0.0356374327776	0.238043253083	-0.162285339141	-0.0825410281408	-0.0818803475992	0.114468117635	0.114222420433	0.256702857537	-0.0837336675691	-0.0523430941378	0.197962446662	0.0322132740807	0.228315367581	27.7606642839	5.68453667174	40.8122292774
13	1.61072261766	-0.437568436343	-0.456664143406	1.31604025423	1.36045302946	2.80323942694	-0.0865855166814	-0.304586789025	0.203191325512	0.278845138981	-0.0379961485639	-0.0125522955094	-0.030567518953	0.0452361585939	0.130331352281	0.338861037439	-0.121410528596	-0.048098712349	0.207074513304	0.0589315992526	0.310876040316	26.7327731609	8.33621267256	52.2300462532
14	1.38696710514	-0.356691526299	-0.520017153163	0.930688450367	0.783099124426	1.71573320123	-0.155813520495	-0.279635857744	-0.102808368552	0.407805616105	0.00348869090845	-0.0816920802043	0.218129772887	0.214194397161	0.12874829921	0.482133265771	-0.0731733386316	-0.0699081506541	0.302602614855	0.0931031879586	0.268749715622	28.1296285142	3.23229819385	58.8647835314
15	1.70428183213	-0.579467772029	-0.658727541866	2.47005354587	1.09012280627	3.38816965741	-0.139491068251	-0.265879392747	0.178890800561	0.202448450096	0.0566264868289	-0.00454028651304	-0.544447356446	0.450520826578	-0.00113092623592	0.466229128771	-0.149302180208	-0.111930908878	0.313541400726	0.00473053946152	0.320917396261	25.616913434	21.2595311264	59.0095785614
16	0.850447294666	-0.0115278458518	0.20982476394	1.52276233458	0.704663337785	2.11134262302	0.0282645256726	-0.0208056843857	-0.116921230559	0.319455533477	-0.135676971076	0.0908189500561	0.443106514271	-0.390680713609	0.10744649732	0.338281232556	-0.144053742886	0.0326120631976	0.34246279605	-0.00252015855299	0.270971515812	6.10647764761	-3.38569875991	39.2594668889
17	1.36558255782	-0.0655823758248	0.202598246809	3.73594247724	1.34118881943	3.60845415528	-0.0599913948474	-0.176986479375	-0.0338398690032	0.59374611238	-0.275317893136	0.281532486666	0.369651915137	-0.929584724932	0.239450679832	0.437611099134	-0.182732120739	0.122360109017	0.712666823478	-0.190781137554	0.365203486238	0.132355865479	5.74447454823	56.6221820266
18	1.25041807431	-0.00887645979665	0.355112805393	1.55142082672	1.67880289097	4.00258959794	-0.0726963069812	-0.344299162558	0.168960073443	0.509841919617	-0.202177070235	0.295996415651	0.137867437594	-0.873124144078	0.14483187484	0.416639880269	-0.0865264202744	0.0746983378076	0.545249489429	-0.0891974120018	0.297588281036	2.06122189687	8.53303472909	54.8027469514
19	0.559253815792	0.0392965103471	-0.766580598841	1.18185113067	1.25108716105	2.52373992667	-0.0755211486884	-0.680561083771	-0.421607435938	1.63334811716	0.0355381894849	-0.306506459874	1.2758829321	-0.0133459944663	0.0416907645842	1.51334248173	-0.191598446832	0.0150738329917	0.740588182717	0.0572922460487	0.522316051078	8.14742614548	-9.09621066869	64.6284418028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 135 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 289 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 290 through 364 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 365 through 395 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 11 through 104 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 135 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 136 through 191 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 192 through 289 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 290 through 341 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 342 through 395 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 13 through 104 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 105 through 191 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 192 through 341 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 342 through 395 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 16 through 113 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 114 through 191 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 192 through 307 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 308 through 391 )

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi