SAXSdb — 6y7v

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

ER lumen protein-retaining receptor 2

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GLU-HIS-ASP-GLU-LEU × 1 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 CARBON DIOXIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERD22_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 1–212

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	6y7v
Deposition date deposition_date	2020-03-02
Structure title title	Crystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0
Keywords keywords	Trafficking receptor; Lipid cubic phase; KDEL receptor, MEMBRANE PROTEIN; MEMBRANE 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.

6y7v__assembly_1__model_1

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

Download this curve (.dat)

6y7v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6y7v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.61 Å
Rg (electron density)	17.73 Å
Total Rg	19.02 Å
Atom count	1920
Residues	215
Excluded volume	36012 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6y7v__assembly_1__model_1`	dimeric （2）	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	ER lumen protein-retaining receptor 2
Molecular weight formula_weight	24476.9 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	2014

MNIFRLTGDLSHLAAIIILLLKIWKSRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIACSYATVYLIYMKFKATYDGNHDTFRVEFLIVPVGGLSFLVNHDFSPLEILWTFSIYLESVAILPQLFMISKTGEAETITTHYLFFLGLYRALYLVNWIWRYYFEGFFDLIAVVAGVVQTVLYCDFFYLYVTKVLKGKKLSLPA

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	GLU-HIS-ASP-GLU-LEU
Molecular weight formula_weight	642.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EHDEL

Entity 3 Entity 3 non-polymer

Description description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CARBON DIOXIDE
Molecular weight formula_weight	44.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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Unit-cell length a length_a	47.620 Å
Unit-cell length b length_b	37.820 Å
Unit-cell length c length_c	62.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.241 Å
Low-resolution limit resolution_low	36.160 Å
R factor r_factor	0.2393
R_work r_work	0.2375
R_free r_free	0.2754

Crystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0

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

ER lumen protein-retaining receptor 2

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

6y7v__assembly_1__model_1

6y7v__assembly_1__model_1 | I(q)

6y7v__assembly_1__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0

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

ER lumen protein-retaining receptor 2

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

6y7v__assembly_1__model_1

6y7v__assembly_1__model_1 | I(q)

6y7v__assembly_1__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)