7ASD

Structure of native royal jelly filaments

PDB DOI: https://doi.org/10.2210/pdb7ASD/pdb
EM Map EMD-11892: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Apis mellifera
Mutation(s): No

Deposited: 2020-10-27 Released: 2020-12-30
Deposition Author(s): Mattei, S., Ban, A., Picenoni, A., Leibundgut, M., Glockshuber, R., Boehringer, D.
Funding Organization(s): European Molecular Biology Organization (EMBO), Human Frontier Science Program (HFSP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of native glycolipoprotein filaments in honeybee royal jelly.

Mattei, S., Ban, A., Picenoni, A., Leibundgut, M., Glockshuber, R., Boehringer, D.

(2020) Nat Commun 11: 6267-6267

PubMed: 33293513 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-20135-x
Primary Citation of Related Structures:
7ASD

PubMed Abstract:
Royal jelly (RJ) is produced by honeybees (Apis mellifera) as nutrition during larval development. The high viscosity of RJ originates from high concentrations of long lipoprotein filaments that include the glycosylated major royal jelly protein 1 (MRJP1), the small protein apisimin and insect lipids. Using cryo-electron microscopy we reveal the architecture and the composition of RJ filaments, in which the MRJP1 forms the outer shell of the assembly, surrounding stacked apisimin tetramers harbouring tightly packed lipids in the centre. The structural data rationalize the pH-dependent disassembly of RJ filaments in the gut of the larvae.

Organizational Affiliation

Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, Zurich, 8093, Switzerland.

Macromolecule Content

Total Structure Weight: 472.08 kDa
Atom Count: 30,296
Modelled Residue Count: 3,664
Deposited Residue Count: 4,080
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major royal jelly protein 1	A [auth AA] C [auth BA] E [auth CA] G [auth DA] I [auth EA] A [auth AA], C [auth BA], E [auth CA], G [auth DA], I [auth EA], K [auth FA], M [auth GA], O [auth HA]	432	Apis mellifera	Mutation(s): 0
UniProt
Find proteins for O18330 (Apis mellifera) Explore O18330 Go to UniProtKB: O18330
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O18330
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apisimin	B [auth AB] D [auth BB] F [auth CB] H [auth DB] J [auth EB] B [auth AB], D [auth BB], F [auth CB], H [auth DB], J [auth EB], L [auth FB], N [auth GB], P [auth HB]	78	Apis mellifera	Mutation(s): 0
UniProt
Find proteins for Q8ISL8 (Apis mellifera) Explore Q8ISL8 Go to UniProtKB: Q8ISL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ISL8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth FAc], CA [auth GAc], EA [auth HAc], Q [auth AAc], S [auth BAc], AA [auth FAc], CA [auth GAc], EA [auth HAc], Q [auth AAc], S [auth BAc], U [auth CAc], W [auth DAc], Y [auth EAc]	2		N-Glycosylation	Interactions Focus chain AA [auth FAc] Focus chain CA [auth GAc] Focus chain EA [auth HAc] Focus chain Q [auth AAc] Focus chain S [auth BAc] Focus chain U [auth CAc] Focus chain W [auth DAc] Focus chain Y [auth EAc] Interactions & Density Focus chain AA [auth FAc] Focus chain CA [auth GAc] Focus chain EA [auth HAc] Focus chain Q [auth AAc] Focus chain S [auth BAc] Focus chain U [auth CAc] Focus chain W [auth DAc] Focus chain Y [auth EAc]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth F], DA [auth G], FA [auth H], R [auth A], T [auth B], BA [auth F], DA [auth G], FA [auth H], R [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]	3		N-Glycosylation	Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
94R Query on 94R Download Ideal Coordinates CCD File SDF format, chain AB [auth FA] SDF format, chain DB [auth FB] SDF format, chain EB [auth GA] SDF format, chain GA [auth AA] SDF format, chain HB [auth GB] SDF format, chain IB [auth HA] SDF format, chain JA [auth AB] SDF format, chain KA [auth BA] SDF format, chain LB [auth HB] SDF format, chain NA [auth BB] SDF format, chain OA [auth CA] SDF format, chain RA [auth CB] SDF format, chain SA [auth DA] SDF format, chain VA [auth DB] SDF format, chain WA [auth EA] SDF format, chain ZA [auth EB] MOL2 format, chain AB [auth FA] MOL2 format, chain DB [auth FB] MOL2 format, chain EB [auth GA] MOL2 format, chain GA [auth AA] MOL2 format, chain HB [auth GB] MOL2 format, chain IB [auth HA] MOL2 format, chain JA [auth AB] MOL2 format, chain KA [auth BA] MOL2 format, chain LB [auth HB] MOL2 format, chain NA [auth BB] MOL2 format, chain OA [auth CA] MOL2 format, chain RA [auth CB] MOL2 format, chain SA [auth DA] MOL2 format, chain VA [auth DB] MOL2 format, chain WA [auth EA] MOL2 format, chain ZA [auth EB]	AB [auth FA] DB [auth FB] EB [auth GA] GA [auth AA] HB [auth GB] AB [auth FA], DB [auth FB], EB [auth GA], GA [auth AA], HB [auth GB], IB [auth HA], JA [auth AB], KA [auth BA], LB [auth HB], NA [auth BB], OA [auth CA], RA [auth CB], SA [auth DA], VA [auth DB], WA [auth EA], ZA [auth EB]	(3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol C₂₈ H₄₆ O INDVLXYUCBVVKW-PXBBAZSNSA-N		Interactions Focus chain AB [auth FA] Focus chain DB [auth FB] Focus chain EB [auth GA] Focus chain GA [auth AA] Focus chain HB [auth GB] Focus chain IB [auth HA] Focus chain JA [auth AB] Focus chain KA [auth BA] Focus chain LB [auth HB] Focus chain NA [auth BB] Focus chain OA [auth CA] Focus chain RA [auth CB] Focus chain SA [auth DA] Focus chain VA [auth DB] Focus chain WA [auth EA] Focus chain ZA [auth EB] Interactions & Density Focus chain AB [auth FA] Focus chain DB [auth FB] Focus chain EB [auth GA] Focus chain GA [auth AA] Focus chain HB [auth GB] Focus chain IB [auth HA] Focus chain JA [auth AB] Focus chain KA [auth BA] Focus chain LB [auth HB] Focus chain NA [auth BB] Focus chain OA [auth CA] Focus chain RA [auth CB] Focus chain SA [auth DA] Focus chain VA [auth DB] Focus chain WA [auth EA] Focus chain ZA [auth EB]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth FA] SDF format, chain FB [auth GA] SDF format, chain HA [auth AA] SDF format, chain JB [auth HA] SDF format, chain LA [auth BA] SDF format, chain PA [auth CA] SDF format, chain TA [auth DA] SDF format, chain XA [auth EA] MOL2 format, chain BB [auth FA] MOL2 format, chain FB [auth GA] MOL2 format, chain HA [auth AA] MOL2 format, chain JB [auth HA] MOL2 format, chain LA [auth BA] MOL2 format, chain PA [auth CA] MOL2 format, chain TA [auth DA] MOL2 format, chain XA [auth EA]	BB [auth FA] FB [auth GA] HA [auth AA] JB [auth HA] LA [auth BA] BB [auth FA], FB [auth GA], HA [auth AA], JB [auth HA], LA [auth BA], PA [auth CA], TA [auth DA], XA [auth EA]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth FA] Focus chain FB [auth GA] Focus chain HA [auth AA] Focus chain JB [auth HA] Focus chain LA [auth BA] Focus chain PA [auth CA] Focus chain TA [auth DA] Focus chain XA [auth EA] Interactions & Density Focus chain BB [auth FA] Focus chain FB [auth GA] Focus chain HA [auth AA] Focus chain JB [auth HA] Focus chain LA [auth BA] Focus chain PA [auth CA] Focus chain TA [auth DA] Focus chain XA [auth EA]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CB [auth FA] SDF format, chain GB [auth GA] SDF format, chain IA [auth AA] SDF format, chain KB [auth HA] SDF format, chain MA [auth BA] SDF format, chain QA [auth CA] SDF format, chain UA [auth DA] SDF format, chain YA [auth EA] MOL2 format, chain CB [auth FA] MOL2 format, chain GB [auth GA] MOL2 format, chain IA [auth AA] MOL2 format, chain KB [auth HA] MOL2 format, chain MA [auth BA] MOL2 format, chain QA [auth CA] MOL2 format, chain UA [auth DA] MOL2 format, chain YA [auth EA]	CB [auth FA] GB [auth GA] IA [auth AA] KB [auth HA] MA [auth BA] CB [auth FA], GB [auth GA], IA [auth AA], KB [auth HA], MA [auth BA], QA [auth CA], UA [auth DA], YA [auth EA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CB [auth FA] Focus chain GB [auth GA] Focus chain IA [auth AA] Focus chain KB [auth HA] Focus chain MA [auth BA] Focus chain QA [auth CA] Focus chain UA [auth DA] Focus chain YA [auth EA] Interactions & Density Focus chain CB [auth FA] Focus chain GB [auth GA] Focus chain IA [auth AA] Focus chain KB [auth HA] Focus chain MA [auth BA] Focus chain QA [auth CA] Focus chain UA [auth DA] Focus chain YA [auth EA]