7bvg

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.

Method: ELECTRON MICROSCOPY

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

Integral membrane indolylacetylinositol arabinosyltransferase EmbA

Mycolicibacterium smegmatis MC2 155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Integral membrane indolylacetylinositol arabinosyltransferase EmbB × 1 （I7GAQ2） Meromycolate extension acyl carrier protein × 1 （A0R0B3） alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose × 1 ;[(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate ; × 1 CARDIOLIPIN × 2 CALCIUM ION × 2 PHOSPHATE ION × 1 4'-PHOSPHOPANTETHEINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R613_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–1088； UniProt 1–1080

Integral membrane indolylacetylinositol arabinosyltransferase EmbB

Mycolicibacterium smegmatis MC2 155

UniProt I7GAQ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Integral membrane indolylacetylinositol arabinosyltransferase EmbA × 1 （A0R613） Meromycolate extension acyl carrier protein × 1 （A0R0B3） alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose × 1 ;[(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate ; × 1 CARDIOLIPIN × 2 CALCIUM ION × 2 PHOSPHATE ION × 1 4'-PHOSPHOPANTETHEINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I7GAQ2_MYCS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1082； UniProt 1–1082

Meromycolate extension acyl carrier protein

OrganismNot specified

UniProt A0R0B3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Integral membrane indolylacetylinositol arabinosyltransferase EmbA × 1 （A0R613） Integral membrane indolylacetylinositol arabinosyltransferase EmbB × 1 （I7GAQ2） alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose × 1 ;[(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate ; × 1 CARDIOLIPIN × 2 CALCIUM ION × 2 PHOSPHATE ION × 1 4'-PHOSPHOPANTETHEINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACPM_MYCS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–99； UniProt 1–99

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	7bvg
Deposition date deposition_date	2020-04-10
Structure title title	Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.
Keywords keywords	;Mycobacterium smegmatis, cell wall synthesis, drug target, ethambutol, arabinosyltransferase, EmbA, EmbB, EmbC, acyl carrier protein, arabinogalactan, lipoarabinomannan, drug resistance, TRANSFERASE ;; TRANSFERASE
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.

7bvg__assembly_1__model_1

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

Download this curve (.dat)

7bvg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7bvg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.66 Å
Rg (electron density)	41.66 Å
Total Rg	42.13 Å
Atom count	17231
Residues	2234
Excluded volume	310110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7bvg__assembly_1__model_1`	trimeric （3）	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 (9)

Entity 1 Entity 1 polymer

Description description	Integral membrane indolylacetylinositol arabinosyltransferase EmbA
Molecular weight formula_weight	116561.9 kDa
EC 编号 ec_number	2.4.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17231

DYKDDDDKMTEPSRIARLIAVVAGIAGVLLCGLVPLLPVEETTATVLWPQGVGADGNVTELTAPLVAGAPRALDVTIPCRAVAELPADGGVVFSTNPAGGIEAGRNGMFIRANADVVYVAFRDTVAAVAPREAVDSGACSEIHVWADVSAVGADFAGIPDASGTLPVDKRPQVSGVFTDLKVPAQPGLAARIDIDTRFITSPTLLKTAVMVLGLACVIGSIVALALLDRGWRRRPPRTRGRAGLWTWITDTGVIGGLLIWHIVGAPTSDDGYNMTIARVASEAGYTTNYYRYFGASEAPFDWYQSVLSHLASISTAGVWMRLPATAAAIATWLIISRCVLPRIGRRVAANRVAMLTAGATFLAAWLPFNNGLRPEPLIAFAVITVWMLVENSIGTRRLWPAAVAIVIAMFSVTLAPQGLIALAPLLVGARAIGRVVTARRAGTGILASLAPLAASVAVVFVIIFRDQTLATVAESVRIKYVVGPTIPWYQEFLRYYFLTVEDSVDGSLTRRFAVLVLLLCLFGLIMVLLRRGRVPGAVSGPLWRLCGSTAIGLLLLILTPTKWAIQFGAFAGLAGALGGVTAFAFARVGLHSRRNLALYVTALLFILAWATSGLNGWFYVGNYGVPWFDKQPVIAHYPVTTIFLVLAIVGGLLAGWLHFRMDYAGHTEVADTGRNRALASTPLLIVATIMVVLELGSMVKATVGRYPVYTVGSANIAALRSAGDSCAMADAVLVEADPNEGMLQPVPGQRFGEYGPLGGEDPVGFTPNGVSDTLEPAEPVAANPGTPNSDGPVDKPNIGIGYAAGTGGGYGPEGVNGSRVFLPFGLDPSRTPVMGSYGENKLAAKATSAWYQLPPRTPDRPLVTVAAAGAIWYYEEDGSFNYGQSLKLQWGVHRPDGTYQALSEVQPIDIFQQKAWRNLRFPLAWAPPEANVARIVADDPNLSEDQWFAFTPPRVPVLQTAQQFLGSQTPVLMDIATAANFPCQRPFAERLGVAELPEYRIIPNFKQMVVSSNQWQSAADGGPFLFIQALLRTEAIPTYLRDDWYRDWGSIERYIRVVPQEQAPTAAIEEGSTRVFGWSRGGPIRALP

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 2 Entity 2 polymer

Description description	Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Molecular weight formula_weight	119077.7 kDa
EC 编号 ec_number	2.4.2.34
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSGNMDEAVSGNMDEAVSAGKDVRIARWVATIAGLLGFVLSVSIPLLPVTQTTATLNWPQQGRLDNVTAPLISQAPLELTATVPCSVVRDLPPEGGLVFGTAPAEGRDAALNAMLVNVTETRVDVIVRNVVVASVNRDRVAGPDCQRIEITSNLDGTYADFVGLTQISGEDAGKLQRTGYPDPNLRPAIVGVFTDLTGPAPQGLSVSAEIDTRFTTHPTALKLAAMLLAIVSTVIALLALWRLDRLDGRRMHRLIPTRWRTVTAVDGVVVGGMAIWYVIGANSSDDGYILQMARTAEHAGYMANYFRWFGSPEDPFGWYYNVLALMTKVSDASIWIRLPDLICALICWLLLSREVLPRLGPAVAGSRAAMWAAGLVLLGAWMPFNNGLRPEGQIATGALITYVLIERAVTSGRLTPAALAITTAAFTLGIQPTGLIAVAALLAGGRPILRIVMRRRRLVGTWPLIAPLLAAGTVILAVVFADQTIATVLEATRIRTAIGPSQEWWTENLRYYYLILPTTDGAISRRVAFVFTAMCLFPSLFMMLRRKHIAGVARGPAWRLMGIIFATMFFLMFTPTKWIHHFGLFAAVGGAMAALATVLVSPTVLRSARNRMAFLSLVLFVLAFCFASTNGWWYVSNFGAPFNNSVPKVGGVQISAIFFALSAIAALWAFWLHLTRRTESRVVDRLTAAPIPVAAGFMVVVMMASMAIGVVRQYPTYSNGWANIRAFAGGCGLADDVLVEPDSNAGFLTPLPGAYGPLGPLGGEDPQGFSPDGVPDRIIAEAIRLNNPQPGTDYDWNRPIKLDEPGINGSTVPLPYGLDPKRVPVAGTYSTEAQQESRLSSAWYELPARDETERAAHPLVVITAAGTITGESVANGLTTGQTVDLEYATRGPDGTLVPAGRVTPYDVGPTPSWRNLRYPRSEIPDDAVAVRVVAEDLSLSQGDWIAVTPPRVPELQSVQEYVGSDQPVLMDWAVGLAFPCQQPMLHANGVTEVPKFRISPDYYAKLQSTDTWQDGINGGLLGITDLLLRASVMSTYLSQDWGQDWGSLRKFDTVVEATPAELDFGSQTHSGLYSPGPLRIRPHLGGIKAFHHHHHHHHHH

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 3 Entity 3 polymer

Description description	Meromycolate extension acyl carrier protein
Molecular weight formula_weight	10743.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MAATQEEIIAGLAEIIEEVTGIEPSEVTPEKSFVDDLDIDSLSMVEIAVQTEDKYGVKIPDEDLAGLRTVGDVVAYIQKLEEENPEAAAALREKFAADQ

Entity 4 Entity 4 branched

Description description	alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose
Molecular weight formula_weight	282.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;[(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate ;
Molecular weight formula_weight	911.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	4'-PHOSPHOPANTETHEINE
Molecular weight formula_weight	358.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d7bvgp_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	7bvgB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	610 — arabinofuranosyltransferase like domain

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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	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	209894

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.

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

Integral membrane indolylacetylinositol arabinosyltransferase EmbA

State in the Current Structure

Other States of the Same Protein in the Database

Integral membrane indolylacetylinositol arabinosyltransferase EmbB

State in the Current Structure

Other States of the Same Protein in the Database

Meromycolate extension acyl carrier protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7bvg__assembly_1__model_1

7bvg__assembly_1__model_1 | I(q)

7bvg__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 (9)

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

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.

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

Integral membrane indolylacetylinositol arabinosyltransferase EmbA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Integral membrane indolylacetylinositol arabinosyltransferase EmbB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Meromycolate extension acyl carrier protein

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

7bvg__assembly_1__model_1

7bvg__assembly_1__model_1 | I(q)

7bvg__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 (9)

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

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)