SAXSdb — 6h9u

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

Endoplasmic reticulum chaperone BiP

Cricetulus griseus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Mesencephalic astrocyte-derived neurotrophic factor × 1 （Q9CXI5） D-MALATE × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIP_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–386； UniProt 28–413

Mesencephalic astrocyte-derived neurotrophic factor

Mus musculus

UniProt Q9CXI5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Endoplasmic reticulum chaperone BiP × 1 （G3I8R9） D-MALATE × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MANF_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–44； UniProt 126–169

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	6h9u
Deposition date deposition_date	2018-08-06
Structure title title	Crystal structure of the BiP NBD and MANF SAP complex
Keywords keywords	MANF, BiP, NDI, HSP70, ARMET, CHAPERONE; CHAPERONE
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.

6h9u__assembly_1__model_1

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

Download this curve (.dat)

6h9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6h9u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.64 Å
Rg (electron density)	22.66 Å
Total Rg	23.50 Å
Atom count	3241
Residues	419
Excluded volume	57686 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6h9u__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	Endoplasmic reticulum chaperone BiP
Molecular weight formula_weight	42557.0 kDa
EC 编号 ec_number	3.6.4.10
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	3591

GTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGD

Source Source

Source organism organism	Cricetulus griseus
Common name common_name	Chinese hamster
NCBI taxonomy ID ncbi_taxonomy_id	10029
Host organism host_organism	Escherichia coli M15

Entity 2 Entity 2 polymer

Description description	Mesencephalic astrocyte-derived neurotrophic factor
Molecular weight formula_weight	5212.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYA

Source Source

Source organism organism	Mus musculus
Common name common_name	House mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	350

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6h9ua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d6h9ua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	6h9uA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	6h9uA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6h9uA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	6h9uA04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

Domain ID domain_id	6h9uB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 — SAP domain

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Unit-cell length a length_a	153.310 Å
Unit-cell length b length_b	66.750 Å
Unit-cell length c length_c	44.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	42.470 Å
R factor r_factor	0.1854
R_work r_work	0.1845
R_free r_free	0.2041

Crystal structure of the BiP NBD and MANF SAP complex

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

Endoplasmic reticulum chaperone BiP

State in the Current Structure

Other States of the Same Protein in the Database

Mesencephalic astrocyte-derived neurotrophic factor

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

6h9u__assembly_1__model_1

6h9u__assembly_1__model_1 | I(q)

6h9u__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) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of the BiP NBD and MANF SAP complex

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

Endoplasmic reticulum chaperone BiP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mesencephalic astrocyte-derived neurotrophic factor

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

6h9u__assembly_1__model_1

6h9u__assembly_1__model_1 | I(q)

6h9u__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) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

7. Citations (1)