8Q54

N5-methyl-H4MPT:CoM methyltransferase -coenzyme M complex + CoM

PDB DOI: https://doi.org/10.2210/pdb8Q54/pdb
EM Map EMD-18162: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Methanothermobacter marburgensis
Mutation(s): No

Deposited: 2023-08-08 Released: 2024-08-21
Deposition Author(s): Aziz, I., Vonck, J., Ermler, U.
Funding Organization(s): Alexander von Humboldt Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex

Aziz, I., Kayastha, K., Kaltwasser, S., Vonck, J., Welsch, S., Murohy, B.J., Kahnt, J., Wu, D., Wagner, T., Shima, S., Ermler, U.

To be published.

Macromolecule Content

Total Structure Weight: 424.26 kDa
Atom Count: 24,599
Modelled Residue Count: 3,156
Deposited Residue Count: 3,861
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit A 1	A, H [auth a], O [auth Q]	238	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for P80184 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P80184 Go to UniProtKB: P80184
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80184
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit B	B, I [auth b], P [auth R]	100	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for Q59584 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore Q59584 Go to UniProtKB: Q59584
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q59584
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit C	C, J [auth c], Q [auth S]	267	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for P80185 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P80185 Go to UniProtKB: P80185
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80185
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit D	D, K [auth d], R [auth T]	233	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for P80183 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P80183 Go to UniProtKB: P80183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80183
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit E	E, L [auth e], S [auth U]	295	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for P80186 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P80186 Go to UniProtKB: P80186
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80186
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit F	F, M [auth f], T [auth V]	68	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for Q50773 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore Q50773 Go to UniProtKB: Q50773
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50773
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahydromethanopterin S-methyltransferase subunit G	G, N [auth g], U [auth W]	86	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for Q50774 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore Q50774 Go to UniProtKB: Q50774
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50774
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JCV Query on JCV Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain EA [auth c] SDF format, chain IA [auth e] SDF format, chain JA [auth e] SDF format, chain KA [auth g] SDF format, chain MA [auth S] SDF format, chain QA [auth U] SDF format, chain RA [auth U] SDF format, chain SA [auth W] SDF format, chain W [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth c] MOL2 format, chain IA [auth e] MOL2 format, chain JA [auth e] MOL2 format, chain KA [auth g] MOL2 format, chain MA [auth S] MOL2 format, chain QA [auth U] MOL2 format, chain RA [auth U] MOL2 format, chain SA [auth W] MOL2 format, chain W [auth C]	AA [auth E] BA [auth E] CA [auth E] EA [auth c] IA [auth e] AA [auth E], BA [auth E], CA [auth E], EA [auth c], IA [auth e], JA [auth e], KA [auth g], MA [auth S], QA [auth U], RA [auth U], SA [auth W], W [auth C]	[(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate C₉₈ H₁₉₃ O₁₉ P JZJZIEMIUITWCY-BEAKYOBHSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth c] Focus chain IA [auth e] Focus chain JA [auth e] Focus chain KA [auth g] Focus chain MA [auth S] Focus chain QA [auth U] Focus chain RA [auth U] Focus chain SA [auth W] Focus chain W [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth c] Focus chain IA [auth e] Focus chain JA [auth e] Focus chain KA [auth g] Focus chain MA [auth S] Focus chain QA [auth U] Focus chain RA [auth U] Focus chain SA [auth W] Focus chain W [auth C]
COM Query on COM Download Ideal Coordinates CCD File SDF format, chain HA [auth e] SDF format, chain PA [auth U] SDF format, chain Z [auth E] MOL2 format, chain HA [auth e] MOL2 format, chain PA [auth U] MOL2 format, chain Z [auth E]	HA [auth e], PA [auth U], Z [auth E]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain HA [auth e] Focus chain PA [auth U] Focus chain Z [auth E] Interactions & Density Focus chain HA [auth e] Focus chain PA [auth U] Focus chain Z [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth b] SDF format, chain LA [auth R] SDF format, chain V [auth B] MOL2 format, chain DA [auth b] MOL2 format, chain LA [auth R] MOL2 format, chain V [auth B]	DA [auth b], LA [auth R], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth b] Focus chain LA [auth R] Focus chain V [auth B] Interactions & Density Focus chain DA [auth b] Focus chain LA [auth R] Focus chain V [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FA [auth e] SDF format, chain GA [auth e] SDF format, chain NA [auth U] SDF format, chain OA [auth U] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain FA [auth e] MOL2 format, chain GA [auth e] MOL2 format, chain NA [auth U] MOL2 format, chain OA [auth U] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	FA [auth e] GA [auth e] NA [auth U] OA [auth U] X [auth E] FA [auth e], GA [auth e], NA [auth U], OA [auth U], X [auth E], Y [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth e] Focus chain GA [auth e] Focus chain NA [auth U] Focus chain OA [auth U] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain FA [auth e] Focus chain GA [auth e] Focus chain NA [auth U] Focus chain OA [auth U] Focus chain X [auth E] Focus chain Y [auth E]