8b01

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc

Method: ELECTRON MICROSCOPY

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

Putative TRAP-type C4-dicarboxylate transport system, small permease component

Photobacterium profundum SS9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Putative TRAP-type C4-dicarboxylate transport system, large permease component × 1 （Q6LPW1） Megabody c7HopQ × 1 （B5Z8H1） N-OCTANE × 6 PHOSPHATIDYLETHANOLAMINE × 2 DOCOSANE × 1 DECANE × 2 SODIUM ION × 2 TRIDECANE × 1 HEXANE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6LPW0_PHOPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 1–169

Putative TRAP-type C4-dicarboxylate transport system, large permease component

Photobacterium profundum SS9

UniProt Q6LPW1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Putative TRAP-type C4-dicarboxylate transport system, small permease component × 1 （Q6LPW0） Megabody c7HopQ × 1 （B5Z8H1） N-OCTANE × 6 PHOSPHATIDYLETHANOLAMINE × 2 DOCOSANE × 1 DECANE × 2 SODIUM ION × 2 TRIDECANE × 1 HEXANE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6LPW1_PHOPR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–426； UniProt 1–426

Megabody c7HopQ

synthetic construct

UniProt B5Z8H1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Putative TRAP-type C4-dicarboxylate transport system, small permease component × 1 （Q6LPW0） Putative TRAP-type C4-dicarboxylate transport system, large permease component × 1 （Q6LPW1） N-OCTANE × 6 PHOSPHATIDYLETHANOLAMINE × 2 DOCOSANE × 1 DECANE × 2 SODIUM ION × 2 TRIDECANE × 1 HEXANE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B5Z8H1_HELPG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 13–233； UniProt 226–446

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	8b01
Deposition date deposition_date	2022-09-06
Structure title title	Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc
Keywords keywords	TRAP, elevator, secondary transporter, sialic acid, TRANSPORT PROTEIN; TRANSPORT 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.

8b01__assembly_1__model_1

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

Download this curve (.dat)

8b01__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8b01__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.57 Å
Rg (electron density)	27.46 Å
Total Rg	28.30 Å
Atom count	5478
Residues	684
Excluded volume	102150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8b01__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 (10)

Entity 1 Entity 1 polymer

Description description	Putative TRAP-type C4-dicarboxylate transport system, small permease component
Molecular weight formula_weight	19748.4 kDa
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	5478

MFRKIIDNIEEIITVPLMIALLCILTWQISSRWLFDSPSLWSEELARVLFLHMAIIGGAIAIKKDDHVKITFFSDKLPRNFRYSLLFALELLVLITIVAMIYYGYAHVQRTAFFELITLGISSSWMTYALPVGGCFMLVRQCQKLYFVLIDWRINENKNTSHLTACDINE

Source Source

Source organism organism	Photobacterium profundum SS9
NCBI taxonomy ID ncbi_taxonomy_id	298386
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Putative TRAP-type C4-dicarboxylate transport system, large permease component
Molecular weight formula_weight	45573.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MFTSIVGWLGLLFAGMPVGFSLIFVGLAFLVLTESTGINFAAQQMIGGLDNFTLLAVPFFVLTGHLMNSAGITERIFNFAKAMVGHITGSLGHVNILASLLFSGMSGSALADAGGLGQLEIKSMRDAKYDDDFAGGLTAASCIIGPLVPPSIPLVIYGVVSNTSIGALFLAGAIPGLLCCIALCIMTYFIAKKRGYMTLPRASRKERLIAFRDAFLSLLTPFIIIGGIFSGKFTPTEAAIISSLYALFLGTVVYKSLTMDKFIKLVQETVTTTSVVALMVMGVTVFGWIVAREQLPQQLAELFLSISDNPLILLLLINLLLLFLGTFIESLALLLLLVPFLVPVATSVGIDPVHFGVMAILNLMIGILTPPMGMALYVVSKVGNIPFHVLTRGVLPLLVPLFIVLGLIIVFPQITLFLPQLVLGYGL

Source Source

Source organism organism	Photobacterium profundum SS9
NCBI taxonomy ID ncbi_taxonomy_id	298386
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Megabody c7HopQ
Molecular weight formula_weight	54867.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLQESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYAGGSLRLSCAASGNIFDRGYMGWYRQAPGKERELVAGISYGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAYPLYDDPYYYWGQGTQVTVSSLE

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	N-OCTANE
Molecular weight formula_weight	114.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	DOCOSANE
Molecular weight formula_weight	310.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	DECANE
Molecular weight formula_weight	142.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	TRIDECANE
Molecular weight formula_weight	184.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	HEXANE
Molecular weight formula_weight	86.2 kDa
Source method src_method	syn
Copy count entity_count	1

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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	—

Resolution resolution	3.03 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	499085

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc

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

Putative TRAP-type C4-dicarboxylate transport system, small permease component

State in the Current Structure

Other States of the Same Protein in the Database

Putative TRAP-type C4-dicarboxylate transport system, large permease component

State in the Current Structure

Other States of the Same Protein in the Database

Megabody c7HopQ

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

8b01__assembly_1__model_1

8b01__assembly_1__model_1 | I(q)

8b01__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 (10)

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 non-polymer

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

Entity 10 Entity 10 non-polymer

7. Citations (1)

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc

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

Putative TRAP-type C4-dicarboxylate transport system, small permease component

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative TRAP-type C4-dicarboxylate transport system, large permease component

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Megabody c7HopQ

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

8b01__assembly_1__model_1

8b01__assembly_1__model_1 | I(q)

8b01__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 (10)

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 non-polymer

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

Entity 10 Entity 10 non-polymer

7. Citations (1)