6ha7

Crystal structure of the BiP NBD and MANF complex

Method: X-RAY DIFFRACTION Dmax: 132.7 Å Quality: GOOD

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

Endoplasmic reticulum chaperone BiP

Cricetulus griseus

UniProt G3I8R9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 28–413 Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;7% PEG6000, 0.1 M Tris-HCl pH7.5 Resolution 2.49 Å R-free 0.256
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 28–413 Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;7% PEG6000, 0.1 M Tris-HCl pH7.5 Resolution 2.49 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BIP_CRIGR
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–387; UniProt 28–413 Author chain B; PDBConstruct 2–387; UniProt 28–413

Mesencephalic astrocyte-derived neurotrophic factor

Mus musculus

UniProt Q9CXI5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 22–179 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;7% PEG6000, 0.1 M Tris-HCl pH7.5 Resolution 2.49 Å R-free 0.256
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 22–179 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;7% PEG6000, 0.1 M Tris-HCl pH7.5 Resolution 2.49 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MANF_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–158; UniProt 22–179 Author chain D; PDBConstruct 1–158; UniProt 22–179

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6ha7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ha7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ha7
Deposition date deposition_date2018-08-07
Structure title titleCrystal structure of the BiP NBD and MANF complex
Keywords keywordsMANF, BiP, NBD, NDI, ARMET, HSP70, CHAPERONE; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.53
Radius of gyration Rg (electron density) rg_electron40.30
Forward intensity I(0) i0206647000.00
Molecular weight molecular_weight116950.0 kDa
Excluded volume excluded_volume146620 ų
Envelope volume envelope_volume207890 ų
Hydration-shell volume shell_volume43915 ų
Envelope diameter envelope_diameter138.8
Shell Rg shell_rg44.34
Envelope Rg envelope_rg39.71
Shape Rg shape_rg40.30
Total Rg total_rg40.52
Total atoms total_atoms8222
Residues n_residues1066
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax132.7
Rg (real space) rg_real40.56
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real2.0660e+08
I(0) uncertainty (real space) i0_real_error3.7300e+06
Rg (reciprocal space) rg_reciprocal40.53
I(0) (reciprocal space) i0_reciprocal206600000.0000
Solution quality estimate total_estimate0.8824
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.8
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.629
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21070000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.790

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6ha7a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd6ha7a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd6ha7a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6ha7b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd6ha7b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd6ha7b3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id6ha7A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id6ha7A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily30
Domain ID domain_id6ha7A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id6ha7A04
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id6ha7B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id6ha7B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily30
Domain ID domain_id6ha7B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id6ha7B04
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4

8. Citations (1)

9. Files and Curves (10)