9qtq

Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tetrahydromethanopterin S-methyltransferase subunit A

Methanosarcina mazei Go1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit B × 3 （P80655） Tetrahydromethanopterin S-methyltransferase subunit C × 3 （O59638） Tetrahydromethanopterin S-methyltransferase subunit D × 3 （P80653） Tetrahydromethanopterin S-methyltransferase subunit E × 3 （P80651） Tetrahydromethanopterin S-methyltransferase subunit F × 3 （P80654） Tetrahydromethanopterin S-methyltransferase subunit G × 3 （P80656） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRA_METMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–240； UniProt 1–240 Author chain B； PDBConstruct 1–240； UniProt 1–240 Author chain C； PDBConstruct 1–240； UniProt 1–240

Tetrahydromethanopterin S-methyltransferase subunit B

Methanosarcina mazei Go1

UniProt P80655

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit A × 3 （O59640） Tetrahydromethanopterin S-methyltransferase subunit C × 3 （O59638） Tetrahydromethanopterin S-methyltransferase subunit D × 3 （P80653） Tetrahydromethanopterin S-methyltransferase subunit E × 3 （P80651） Tetrahydromethanopterin S-methyltransferase subunit F × 3 （P80654） Tetrahydromethanopterin S-methyltransferase subunit G × 3 （P80656） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRB_METMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–108； UniProt 1–108 Author chain E； PDBConstruct 1–108； UniProt 1–108 Author chain F； PDBConstruct 1–108； UniProt 1–108

Tetrahydromethanopterin S-methyltransferase subunit C

Methanosarcina mazei Go1

UniProt O59638

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit A × 3 （O59640） Tetrahydromethanopterin S-methyltransferase subunit B × 3 （P80655） Tetrahydromethanopterin S-methyltransferase subunit D × 3 （P80653） Tetrahydromethanopterin S-methyltransferase subunit E × 3 （P80651） Tetrahydromethanopterin S-methyltransferase subunit F × 3 （P80654） Tetrahydromethanopterin S-methyltransferase subunit G × 3 （P80656） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRC_METMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–267； UniProt 1–267 Author chain H； PDBConstruct 1–267； UniProt 1–267 Author chain I； PDBConstruct 1–267； UniProt 1–267

Tetrahydromethanopterin S-methyltransferase subunit D

Methanosarcina mazei Go1

UniProt P80653

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit A × 3 （O59640） Tetrahydromethanopterin S-methyltransferase subunit B × 3 （P80655） Tetrahydromethanopterin S-methyltransferase subunit C × 3 （O59638） Tetrahydromethanopterin S-methyltransferase subunit E × 3 （P80651） Tetrahydromethanopterin S-methyltransferase subunit F × 3 （P80654） Tetrahydromethanopterin S-methyltransferase subunit G × 3 （P80656） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRD_METMA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain J； PDBConstruct 1–250； UniProt 1–250 Author chain K； PDBConstruct 1–250； UniProt 1–250 Author chain L； PDBConstruct 1–250； UniProt 1–250

Tetrahydromethanopterin S-methyltransferase subunit E

Methanosarcina mazei Go1

UniProt P80651

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit A × 3 （O59640） Tetrahydromethanopterin S-methyltransferase subunit B × 3 （P80655） Tetrahydromethanopterin S-methyltransferase subunit C × 3 （O59638） Tetrahydromethanopterin S-methyltransferase subunit D × 3 （P80653） Tetrahydromethanopterin S-methyltransferase subunit F × 3 （P80654） Tetrahydromethanopterin S-methyltransferase subunit G × 3 （P80656） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRE_METMA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–304； UniProt 1–304 Author chain N； PDBConstruct 1–304； UniProt 1–304 Author chain O； PDBConstruct 1–304； UniProt 1–304

Tetrahydromethanopterin S-methyltransferase subunit F

Methanosarcina mazei Go1

UniProt P80654

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit A × 3 （O59640） Tetrahydromethanopterin S-methyltransferase subunit B × 3 （P80655） Tetrahydromethanopterin S-methyltransferase subunit C × 3 （O59638） Tetrahydromethanopterin S-methyltransferase subunit D × 3 （P80653） Tetrahydromethanopterin S-methyltransferase subunit E × 3 （P80651） Tetrahydromethanopterin S-methyltransferase subunit G × 3 （P80656） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRF_METMA
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain P； PDBConstruct 1–72； UniProt 1–72 Author chain Q； PDBConstruct 1–72； UniProt 1–72 Author chain R； PDBConstruct 1–72； UniProt 1–72

Tetrahydromethanopterin S-methyltransferase subunit G

Methanosarcina mazei Go1

UniProt P80656

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	Tetrahydromethanopterin S-methyltransferase subunit A × 3 （O59640） Tetrahydromethanopterin S-methyltransferase subunit B × 3 （P80655） Tetrahydromethanopterin S-methyltransferase subunit C × 3 （O59638） Tetrahydromethanopterin S-methyltransferase subunit D × 3 （P80653） Tetrahydromethanopterin S-methyltransferase subunit E × 3 （P80651） Tetrahydromethanopterin S-methyltransferase subunit F × 3 （P80654） 2-Hydroxy-archaetidylinositol × 6 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL × 3 Archaetidylinositol × 3 SODIUM ION × 3 Archaetidylethanolamine × 3 water × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRG_METMA
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain S； PDBConstruct 1–72； UniProt 1–72 Author chain T； PDBConstruct 1–72； UniProt 1–72 Author chain U； PDBConstruct 1–72； UniProt 1–72

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9qtq
Deposition date deposition_date	2025-04-09
Structure title title	Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Keywords keywords	;Sodium-pumping, membrane-bound, methyltransferase complex, methanogen, methanogenic, methylotrophic, archaeon, archaea, methanosarcina, methanosarcina mazei, Vitamin B12, corrinoid, cobalt, 5-hydroxybenzimidazole, small protein, oxygen-sensitive, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9qtq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9qtq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qtq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	42.12 Å
Rg (electron density)	41.87 Å
Total Rg	42.58 Å
Atom count	26010
Residues	3231
Excluded volume	448110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qtq__assembly_1__model_1`	21-meric （21）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit A
Molecular weight formula_weight	25395.2 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	28650

MADKREPAPGWPILKGEYEVGDVKNSVLVITCGSHLPGKPILDAGAACTGSCKTENLGIEKVVAHIISNPNIRYLLVTGSEVKGHITGQSMMSLHANGVKENRIAGALGAIPYVENLNAAAVARFQEQVQVVNLLDTEDMGAITSKVRELASKDPGAFDADPLVVEISEEGEEEEEGGVVRPVSGEIAVLRSRLKAIEARMMDIGNLNKFHSGVHAGKVEGAMIGLTITISLLGLLLLGR

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrA
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 2 Entity 2 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit B
Molecular weight formula_weight	11879.6 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MSIVRIAPEINLVMDTESGTVTQERKDSIQYSMEPVFERVDKLDAIADDLVNSLSPSKPLLNTWPGRENTSYIAGIYSNSFYGIIVGLAFSGLLALIIYITRLMGGVV

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrB
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 3 Entity 3 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit C
Molecular weight formula_weight	26953.9 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

MSAGGAGGEAKGAYPQQTLMALGIVGGLVGIYLGHFMPPAYSFFGGIGAICATVWGADAVRRVASYGLGTGVPSIGMLALGMGILAALFGLALGGIAGPILAVVVAAIIGGVIGALANKVIGMGIPIMEQAMIEISCAGTLVILGLSVVIAGSFDYAAIIENVIANGYIALIFIIGGMGILHPFNACLGPDESQDRTLILAVEKAAIALIITGFASSLHEGLMTAGINILVGLVIWYVAFSKYYALIKRDAYAVVGTGLLPSAEELQ

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrC
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 4 Entity 4 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit D
Molecular weight formula_weight	25279.8 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L

MIDAILGNILWMVFIIIGGVLISWGVHFVPVGGAPAAMAQATGVGTGTVQLATGAGLTGLVSAGFMMNVTDNFPLIVASGAVGAMIMIAVTMIVGTWIYVYGVGCVPSSAKVKVDPITKYRQDLYVSQGTEGHGIPTVSFVSGVIGAALGGIGGSLIYYSLIEVGVSVGLERVGVTSAVTGNSLVAVAAIFAIGIFLVNAVIPSYNIGGTIEGFHDPKFKKWPKAVISSVVASILCAIVAVIAIAQLGGI

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrD
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 5 Entity 5 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit E
Molecular weight formula_weight	35539.6 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O

MEPLIGMGVLALIGVAATIAGASEDLESDIGSQSNPNSQVQLAPQMMFPHRIFNKAISGEPPSNALMCSIGAAIATVLISEFTVSPLFALVFGSVIAASVHATFAVTATMGRCASQSRFKQPIYLDMIRSHTPAIMGYAFITTFCVLIVSYLMTVVLGHPFPLTMLAFIWGITIGAIGSSTGDVHYGAEREFQQFEFGSGLNASNSGNIVRYAESGLRNGFDNSWFCSKFGGPTTGIAFGMTVFLGSWITTIFDPAQGLSMGWLSVIAGVIIVLILIIWNWKIEVQARKAYGPYKEDKAEEASASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrE
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 6 Entity 6 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit F
Molecular weight formula_weight	7574.0 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R

MAEEHEKGVPMVLAPQMGAIDATVESIRYRAQLIARNQKLDSGVAATGIIGFAAGFLFSLLMVIVLPVAVGL

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrF
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 7 Entity 7 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit G
Molecular weight formula_weight	8030.4 kDa
EC 编号 ec_number	7.2.1.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T,U

MDGKAPAAFVEPGEFNEVMKRLDQIDEKVEFVNSEVAQRIGKKVGRDIGILYGGVIGLLLFLIYVQISSMFM

Source Source

Source organism organism	Methanosarcina mazei Go1
Common name common_name	MtrG
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Methanosarcina mazei Go1

Entity 8 Entity 8 non-polymer

Description description	2-Hydroxy-archaetidylinositol
Molecular weight formula_weight	836.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
Molecular weight formula_weight	733.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	Archaetidylinositol
Molecular weight formula_weight	911.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 12 Entity 12 non-polymer

Description description	Archaetidylethanolamine
Molecular weight formula_weight	776.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2640

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	136531

Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tetrahydromethanopterin S-methyltransferase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetrahydromethanopterin S-methyltransferase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetrahydromethanopterin S-methyltransferase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetrahydromethanopterin S-methyltransferase subunit D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetrahydromethanopterin S-methyltransferase subunit E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetrahydromethanopterin S-methyltransferase subunit F

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetrahydromethanopterin S-methyltransferase subunit G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qtq__assembly_1__model_1

9qtq__assembly_1__model_1 | I(q)

9qtq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source