SAXSdb — 7jmd

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

Gap junction alpha-3 protein

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–413 Chain B； UniProt 1–413 Chain C； UniProt 1–413 Chain D； UniProt 1–413 Chain E； UniProt 1–413 Chain F； UniProt 1–413 Chain G； UniProt 1–413 Chain H； UniProt 1–413 Chain I； UniProt 1–413 Chain J； UniProt 1–413 Chain K； UniProt 1–413 Chain L； UniProt 1–413	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 132	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7JMD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6MHQ Structure of connexin-46 intercellular gap junction channel at 3.4 angstrom resolution by cryoEM Deposited 2018-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–348（348 aa） Chain B 1–348（348 aa） Chain C 1–348（348 aa） Chain D 1–348（348 aa） Chain E 1–348（348 aa） Chain F 1–348（348 aa） Chain G 1–348（348 aa） Chain H 1–348（348 aa） Chain I 1–348（348 aa） Chain J 1–348（348 aa） Chain K 1–348（348 aa） Chain L 1–348（348 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；10 sec wait before blotting, 4.0 second blot before plunging	Resolution 3.40 Å
7JKC Sheep Connexin-46 at 1.9 angstroms resolution by CryoEM Deposited 2020-07-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 180	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.90 Å
7JN0 Sheep Connexin-46 at 2.5 angstroms resolution, Lipid Class 2 Deposited 2020-08-03	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 168	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7JN1 Sheep Connexin-46 at 2.5 angstroms resolution, Lipid Class 3 Deposited 2020-08-03	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 144	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9Z7P Stable open sheep connexin-46 in amphipol at low pH Deposited 2025-11-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 5.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9Z81 Stable open state sheep connexin-46 in DMPC nanodiscs at neutral pH Deposited 2025-11-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 312	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.00 Å
9Z8F Destabilized open state sheep connexin-46 in DMPC nanodiscs at neutral pH Deposited 2025-11-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 276	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
9Z8M Gated state sheep connexin-46 in DMPC nanodiscs at neutral pH Deposited 2025-11-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 192	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9Z9G Stable open state sheep connexin-46 in DMPC nanodiscs at low pH Deposited 2025-11-18	Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 180	ELECTRON MICROSCOPY cryo-EM buffer pH 5.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9Z9S Destabilized open state sheep connexin-46 in DMPC nanodiscs at low pH Deposited 2025-11-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 288	ELECTRON MICROSCOPY cryo-EM buffer pH 5.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
9Z9X Gated state sheep connexin-46 in DMPC nanodiscs at low pH Deposited 2025-11-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 396	ELECTRON MICROSCOPY cryo-EM buffer pH 5.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9ZA3 Asymmetrically gated state sheep connexin-46 in DMPC nanodiscs at low pH Deposited 2025-11-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa） Chain C 1–413（413 aa） Chain D 1–413（413 aa） Chain E 1–413（413 aa） Chain F 1–413（413 aa） Chain G 1–413（413 aa） Chain H 1–413（413 aa） Chain I 1–413（413 aa） Chain J 1–413（413 aa） Chain K 1–413（413 aa） Chain L 1–413（413 aa）	Not recorded	MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 252	ELECTRON MICROSCOPY cryo-EM buffer pH 5.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CXA3_SHEEP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–413； UniProt 1–413 Author chain B； PDBConstruct 1–413； UniProt 1–413 Author chain C； PDBConstruct 1–413； UniProt 1–413 Author chain D； PDBConstruct 1–413； UniProt 1–413 Author chain E； PDBConstruct 1–413； UniProt 1–413 Author chain F； PDBConstruct 1–413； UniProt 1–413 Author chain G； PDBConstruct 1–413； UniProt 1–413 Author chain H； PDBConstruct 1–413； UniProt 1–413 Author chain I； PDBConstruct 1–413； UniProt 1–413 Author chain J； PDBConstruct 1–413； UniProt 1–413 Author chain K； PDBConstruct 1–413； UniProt 1–413 Author chain L； PDBConstruct 1–413； UniProt 1–413

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	7jmd
Deposition date deposition_date	2020-07-31
Structure title title	Sheep Connexin-46 at 2.5 angstroms resolution, Lipid Class 1
Keywords keywords	Connexin, Gap Junction, Lipid, Nanodisc, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	46.72 Å
Radius of gyration Rg (electron density) rg_electron	47.81 Å
Forward intensity I(0) i0	856322000.00
Molecular weight molecular_weight	303290.0 kDa
Excluded volume excluded_volume	404390 Å³
Envelope volume envelope_volume	518980 Å³
Hydration-shell volume shell_volume	88943 Å³
Envelope diameter envelope_diameter	167.6 Å
Shell Rg shell_rg	52.84 Å
Envelope Rg envelope_rg	48.02 Å
Shape Rg shape_rg	47.83 Å
Total Rg total_rg	47.93 Å
Total atoms total_atoms	44592
Residues n_residues	2316
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	164.6 Å
Rg (real space) rg_real	47.08 Å
Rg uncertainty (real space) rg_real_error	1.89 Å
I(0) (real space) i0_real	8.5630e+08
I(0) uncertainty (real space) i0_real_error	1.6900e+07
Rg (reciprocal space) rg_reciprocal	46.72 Å
I(0) (reciprocal space) i0_reciprocal	855900000.0000
Solution quality estimate total_estimate	0.8120
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.4 Å
Skewness Skewness skewness	0.584
Kurtosis Kurtosis kurtosis	-0.188
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	235700000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.578; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.826

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Gap junction alpha-3 protein
Molecular weight formula_weight	44033.0 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	44796

MGDWSFLGRLLENAQEHSTVIGKVWLTVLFIFRILVLGAAAEEVWGDEQSDFTCNTQQPGCENVCYDRAFPISHVRFWVLQIIFVSTPTLIYLGHVLHLVRMEEKRKEREEEPPKAAGPAEEHQDPAPVRDDRGKVRIAGALLRTYVFNIIFKTLFEVGFIAGQYFLYGFQLKPLYRCDRWPCPNTVDCFISRPTEKTIFILFMLAVACVSLLLNVLEIYHLGWKKLKQGMTSPFRPDTPGSRAGSAKPMGGSPLLLPPNSAPPAVTIGFPPYYAPSASSLGQASAPGYPEPPLPAALPGTPGTPGTPGTLGGGGGNQGLRAPAQNCANREAEPQTSARKASPPASTPPAAPAGGPQQFLPGGAAGSSGDSDGEGAVTAVELHAPPEPPADPGRSSKASKSSGGRARAADLAI

Entity 2 Entity 2 non-polymer

Description description	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	677.9 kDa
Source method src_method	syn
Copy count entity_count	132

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	7jmdA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdI01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdJ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdK01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

Domain ID domain_id	7jmdL01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	80 — Gap junction channel protein cysteine-rich domain

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8. Citations (2)

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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	2.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	6073

fit	/app/data/saxs_computation/jm/7jmd/7jmd.fit
pddf	/app/data/pr_computation/jm/7jmd/7jmd.pr.out
profile	/app/data/saxs_computation/jm/7jmd/7jmd.dat

Sheep Connexin-46 at 2.5 angstroms resolution, Lipid Class 1

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

Gap junction alpha-3 protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D