4jc6

Mercury activation of the plant aquaporin SoPIP2;1 - structural and functional characterization

Method: X-RAY DIFFRACTION

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

Aquaporin

Spinacia oleracea

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	octyl beta-D-glucopyranoside × 6 CADMIUM ION × 9 MERCURY (II) ION × 16 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	octyl beta-D-glucopyranoside × 7 CADMIUM ION × 8 MERCURY (II) ION × 16 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q41372_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 1–281 Author chain B； PDBConstruct 1–281； UniProt 1–281 Author chain C； PDBConstruct 1–281； UniProt 1–281 Author chain D； PDBConstruct 1–281； UniProt 1–281 Author chain H； PDBConstruct 1–281； UniProt 1–281 Author chain J； PDBConstruct 1–281； UniProt 1–281 Author chain L； PDBConstruct 1–281； UniProt 1–281 Author chain N； PDBConstruct 1–281； UniProt 1–281

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	4jc6
Deposition date deposition_date	2013-02-21
Structure title title	Mercury activation of the plant aquaporin SoPIP2;1 - structural and functional characterization
Keywords keywords	Membrane protein, aquaporin, mercury, cadmium, Transport Protein; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

4jc6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4jc6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jc6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.29 Å
Rg (electron density)	27.32 Å
Total Rg	28.29 Å
Atom count	7674
Residues	1003
Excluded volume	141110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jc6__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4jc6__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Aquaporin
Molecular weight formula_weight	29929.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,H,J,L,N
Atom count atom_count	15969

MSKEVSEEAQAHQHGKDYVDPPPAPFFDLGELKLWSFWRAAIAEFIATLLFLYITVATVIGHSKETVVCGSVGLLGIAWAFGGMIFVLVYCTAGISGGHINPAVTFGLFLARKVSLLRALVYMIAQCLGAICGVGLVKAFMKGPYNQFGGGANSVALGYNKGTALGAEIIGTFVLVYTVFSATDPKRSARDSHVPILAPLPIGFAVFMVHLATIPITGTGINPARSFGAAVIFNSNKVWDDQWIFWVGPFIGAAVAAAYHQYVLRAAAIKALGSFRSNPTN

Source Source

Source organism organism	Spinacia oleracea
Common name common_name	Spinach
NCBI taxonomy ID ncbi_taxonomy_id	3562
Host organism host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	32

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	616

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4jc6a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6c_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6d_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6h_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6j_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6l_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

Domain ID domain_id	d4jc6n_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.19 — Aquaporin-like
Superfamily Superfamily superfamily	f.19.1 — Aquaporin-like
Family Family family	f.19.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4jc6A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6H00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6J00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6L00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

Domain ID domain_id	4jc6N00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1080 — Glycerol uptake facilitator protein
Homologous superfamily homologous superfamily	10 — Glycerol uptake facilitator protein.

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Unit-cell length a length_a	123.546 Å
Unit-cell length b length_b	141.818 Å
Unit-cell length c length_c	186.515 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.152 Å
Low-resolution limit resolution_low	29.900 Å
R factor r_factor	0.1984
R_work r_work	0.1969
R_free r_free	0.2270

Mercury activation of the plant aquaporin SoPIP2;1 - structural and functional characterization

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

Aquaporin

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

4jc6__assembly_2__model_1

4jc6__assembly_2__model_1 | I(q)

4jc6__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Mercury activation of the plant aquaporin SoPIP2;1 - structural and functional characterization

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

Aquaporin

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

4jc6__assembly_2__model_1

4jc6__assembly_2__model_1 | I(q)

4jc6__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)