SAXSdb — 4ygd

▼

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

Protein ERGIC-53

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Multiple coagulation factor deficiency protein 2 × 1 （Q8NI22） CALCIUM ION × 4 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Multiple coagulation factor deficiency protein 2 × 1 （Q8NI22） CALCIUM ION × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Multiple coagulation factor deficiency protein 2 × 1 （Q8NI22） CALCIUM ION × 4 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Multiple coagulation factor deficiency protein 2 × 1 （Q8NI22） CALCIUM ION × 4 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LMAN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–246； UniProt 31–269 Author chain C； PDBConstruct 8–246； UniProt 31–269 Author chain E； PDBConstruct 8–246； UniProt 31–269 Author chain G； PDBConstruct 8–246； UniProt 31–269

Multiple coagulation factor deficiency protein 2

Homo sapiens

UniProt Q8NI22

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein ERGIC-53 × 1 （P49257） CALCIUM ION × 4 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein ERGIC-53 × 1 （P49257） CALCIUM ION × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Protein ERGIC-53 × 1 （P49257） CALCIUM ION × 4 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein ERGIC-53 × 1 （P49257） CALCIUM ION × 4 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCFD2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 25–104； UniProt 67–146 Author chain D； PDBConstruct 25–104； UniProt 67–146 Author chain F； PDBConstruct 25–104； UniProt 67–146 Author chain H； PDBConstruct 25–104； UniProt 67–146

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ygd
Deposition date deposition_date	2015-02-26
Structure title title	Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2
Keywords keywords	BETA-SANDWICH, EF-HAND, CARGO RECEPTOR, CALCIUM BINDING, ER, ERGIC, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4ygd__assembly_1__model_1

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

Download this curve (.dat)

4ygd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ygd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.68 Å
Rg (electron density)	19.64 Å
Total Rg	20.69 Å
Atom count	2343
Residues	296
Excluded volume	41240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ygd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ygd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ygd__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4ygd__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein ERGIC-53
Molecular weight formula_weight	27154.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	9564

MNHKVHMDGVGGDPAVALPHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDNDGKKNNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Multiple coagulation factor deficiency protein 2
Molecular weight formula_weight	12056.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MGHHHHHHHHHHSSGHIEGRHMLEMSPQELQLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGSEQAPLMSEDELINIIDGVLRDDDKNNDGYIDYAEFAKSLQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	293

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ygda_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.13 — Lectin leg-like

Domain ID domain_id	d4ygdc_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.13 — Lectin leg-like

Domain ID domain_id	d4ygde_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.13 — Lectin leg-like

Domain ID domain_id	d4ygdg_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.13 — Lectin leg-like

CATH v4.4 (8 domains)

Domain ID domain_id	4ygdA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4ygdB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4ygdC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4ygdD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4ygdE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4ygdF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4ygdG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4ygdH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

▶

Unit-cell length a length_a	103.063 Å
Unit-cell length b length_b	58.765 Å
Unit-cell length c length_c	119.386 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1950
R_work r_work	0.1930
R_free r_free	0.2320

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2

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

Protein ERGIC-53

State in the Current Structure

Other States of the Same Protein in the Database

Multiple coagulation factor deficiency protein 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

4ygd__assembly_1__model_1

4ygd__assembly_1__model_1 | I(q)

4ygd__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2

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

Protein ERGIC-53

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Multiple coagulation factor deficiency protein 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

4ygd__assembly_1__model_1

4ygd__assembly_1__model_1 | I(q)

4ygd__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)