SAXSdb — 7rxc

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

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Streptococcus sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Fab_8D3_2 heavy chain × 1 Fab_8D3_2 light chain × 1 Nb_KR × 1 ER lumen protein-retaining receptor 2 × 1 （Q5ZKX9） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A4Z0THX4_ECOLX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 2–359； UniProt 27–384

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Streptococcus sp.

UniProt P06654

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Fab_8D3_2 heavy chain × 1 Fab_8D3_2 light chain × 1 Nb_KR × 1 ER lumen protein-retaining receptor 2 × 1 （Q5ZKX9） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPG1_STRSG
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 479–536； UniProt 295–352

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Streptococcus sp.

UniProt P99134

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Fab_8D3_2 heavy chain × 1 Fab_8D3_2 light chain × 1 Nb_KR × 1 ER lumen protein-retaining receptor 2 × 1 （Q5ZKX9） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPA_STAAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 360–467； UniProt 43–151

ER lumen protein-retaining receptor 2

Gallus gallus

UniProt Q5ZKX9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Fab_8D3_2 heavy chain × 1 Fab_8D3_2 light chain × 1 Nb_KR × 1 Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G × 1 （A0A4Z0THX4,P06654,P99134） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4	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	5
Chains and sequence ranges	Author chain K； 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	7rxc
Deposition date deposition_date	2021-08-22
Structure title title	CryoEM structure of KDELR with Legobody
Keywords keywords	protein A, maltose-binding protein, Fab, nanobody, STRUCTURAL PROTEIN; STRUCTURAL 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.

7rxc__assembly_1__model_1

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

Download this curve (.dat)

7rxc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7rxc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.05 Å
Rg (electron density)	43.36 Å
Total Rg	43.58 Å
Atom count	9360
Residues	1178
Excluded volume	167840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7rxc__assembly_1__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	Fab_8D3_2 heavy chain
Molecular weight formula_weight	25252.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	9360

DVQLVESGGGLVQPGKSLRLSCAASGFTFSNFGMHWVRQAPEMGLEWVAYISSGSTTKYYGDTVKGRFTISRDNPKNTLYLQMNSLRSEDTAMYYCARRPLYDGDYGYPMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Fab_8D3_2 light chain
Molecular weight formula_weight	24095.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

NIMLTQSPSSLAVSAGERVTMSCKSTQSILYNSNQKTYLAWYQQKPGQSPKLLIYWASTRASGVPDRFTGSGSGTDFTLTINSVQPEDLAVYYCHQYLSAWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Nb_KR
Molecular weight formula_weight	14698.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

QVQLVESGGGLVQAGGSLRLSCAASGFPVKRWSMTWYRQAPGKEREWVAAIRSAGHWTHYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNVKDEGDFSYWYDYWGQGTQVTVSSLEHHHHHH

Source Source

Source organism organism	Vicugna pacos
Common name common_name	Alpaca, Lama pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
Molecular weight formula_weight	59233.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDQALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNEHQAPKGGSGGAGSGDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAGGGSGGGSGGSAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEGSGHHHHHH

Source Source

Source organism organism	Streptococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	1306
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	ER lumen protein-retaining receptor 2
Molecular weight formula_weight	30084.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNIFRLTGDLSHLAAIIILLLKIWKSRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIACSYATVYLIYMKFKATYDGNHDTFRVEFLIVPVGGLSFLVNHDFSPLEILWTFSIYLESVAILPQLFMISKTGEAETITTHYLFFLGLYRALYLVNWIWRYYFEGFFDLIAVVAGVVQTVLYCDFFYLYVTKVLKGKKLSLPAGSGGENLYFQSGGGMDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP

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 6 Entity 6 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	760.1 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	7rxcB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	7rxcH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7rxcH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7rxcL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7rxcL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7rxcN01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	246878

CryoEM structure of KDELR with Legobody

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

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

7rxc__assembly_1__model_1

7rxc__assembly_1__model_1 | I(q)

7rxc__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)