SAXSdb — 8ffo

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

Transient receptor potential cation channel subfamily V member 5

Oryctolagus cuniculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ERGOSTEROL × 8 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 ;[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate ; × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRPV5_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–730； UniProt 1–730 Author chain B； PDBConstruct 1–730； UniProt 1–730 Author chain C； PDBConstruct 1–730； UniProt 1–730 Author chain D； PDBConstruct 1–730； UniProt 1–730

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	8ffo
Deposition date deposition_date	2022-12-09
Last revision last_revision	2023-11-01
Structure title title	Cryo-EM structure of wildtype rabbit TRPV5 with PI(4,5)P2 in nanodiscs
Keywords keywords	TRPV5, TRP Channel, PI(4, 5)P2, 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.

8ffo__assembly_1__model_1

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

Download this curve (.dat)

8ffo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ffo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.69 Å
Rg (electron density)	45.57 Å
Total Rg	45.82 Å
Atom count	20100
Residues	2416
Excluded volume	365820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ffo__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Transient receptor potential cation channel subfamily V member 5
Molecular weight formula_weight	83784.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20100

MGACPPKAKGPWAQLQKLLISWPVGEQDWEQYRDRVNMLQQERIRDSPLLQAAKENDLRLLKILLLNQSCDFQQRGAVGETALHVAALYDNLEAATLLMEAAPELAKEPALCEPFVGQTALHIAVMNQNLNLVRALLARGASVSARATGAAFRRSPHNLIYYGEHPLSFAACVGSEEIVRLLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDEHSDHLQSLELVPNHQGLTPFKLAGVEGNTVMFQHLMQKRKHVQWTCGPLTSTLYDLTEIDSWGEELSFLELVVSSKKREARQILEQTPVKELVSFKWKKYGRPYFCVLASLYILYMICFTTCCIYRPLKLRDDNRTDPRDITILQQKLLQEAYVTHQDNIRLVGELVTVTGAVIILLLEIPDIFRVGASRYFGQTILGGPFHVIIITYASLVLLTMVMRLTNMNGEVVPLSFALVLGWCSVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFHITFQTEDPNNLGEFSDYPTALFSTFELFLTIIDGPANYSVDLPFMYCITYAAFAIIATLLMLNLFIAMMGDTHWRVAQERDELWRAQVVATTVMLERKMPRFLWPRSGICGYEYGLGDRWFLRVENHHDQNPLRVLRYVEAFKCSDKEDGQEQLSEKRPSTVESGMLSRASVAFQTPSLSRTTSQSSNSHRGWEILRRNTLGHLNLGLDLGEGDGEEVYHFTETSQVAPA

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 non-polymer

Description description	ERGOSTEROL
Molecular weight formula_weight	396.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	758.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	;[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate ;
Molecular weight formula_weight	746.6 kDa
Source method src_method	syn
Copy count entity_count	4

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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	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	115278

Cryo-EM structure of wildtype rabbit TRPV5 with PI(4,5)P2 in nanodiscs

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

Transient receptor potential cation channel subfamily V member 5

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

8ffo__assembly_1__model_1

8ffo__assembly_1__model_1 | I(q)

8ffo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

Cryo-EM structure of wildtype rabbit TRPV5 with PI(4,5)P2 in nanodiscs

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

Transient receptor potential cation channel subfamily V member 5

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

8ffo__assembly_1__model_1

8ffo__assembly_1__model_1 | I(q)

8ffo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)