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- PDB-5yyl: Structure of Major Royal Jelly Protein 1 Oligomer -

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Basic information

Entry
Database: PDB / ID: 5yyl
TitleStructure of Major Royal Jelly Protein 1 Oligomer
Components
  • Apisimin
  • Major royal jelly protein 1
KeywordsSIGNALING PROTEIN / Complex / Royal jelly
Function / homology
Function and homology information


caste determination, influence by environmental factors / defense response to fungus / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Major royal jelly protein/protein yellow / Major royal jelly protein / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
(3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol / Major royal jelly protein 1 / Apisimin
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsTian, W. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2016YFC1200400 China
CitationJournal: Nat Commun / Year: 2018
Title: Architecture of the native major royal jelly protein 1 oligomer.
Authors: Tian, W. / Li, M. / Guo, H. / Peng, W. / Xue, X. / Hu, Y. / Liu, Y. / Zhao, Y. / Fang, X. / Wang, K. / Li, X. / Tong, Y. / Conlon, M.A. / Wu, W. / Ren, F. / Chen, Z.
History
DepositionDec 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major royal jelly protein 1
B: Major royal jelly protein 1
C: Apisimin
D: Apisimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,00910
Polymers113,7684
Non-polymers2,2406
Water2,594144
1
A: Major royal jelly protein 1
B: Major royal jelly protein 1
C: Apisimin
D: Apisimin
hetero molecules

A: Major royal jelly protein 1
B: Major royal jelly protein 1
C: Apisimin
D: Apisimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,01720
Polymers227,5378
Non-polymers4,48112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area15820 Å2
ΔGint-81 kcal/mol
Surface area68590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.582, 211.582, 149.968
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

21A-667-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A28 - 432
2010B28 - 432
1020C37 - 76
2020D37 - 76

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Major royal jelly protein 1 / MRJP-1 / 56-kDa protein 4 / p56kP-4 / Bee-milk protein / Royalactin


Mass: 48934.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / References: UniProt: O18330
#2: Protein Apisimin / Apisimin / Uncharacterized protein


Mass: 7949.325 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / References: UniProt: Q8ISL8

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][<C4N1O2>]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 148 molecules

#4: Chemical
ChemComp-94R / (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol / 24-methylenecholesterol


Mass: 398.664 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H46O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 37682 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rsym value: 0.099 / Net I/σ(I): 20.46
Reflection shellResolution: 2.65→2.7 Å / Rsym value: 3.019

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.932 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.823 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1605 5 %RANDOM
Rwork0.239 ---
obs0.241 30696 86.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 146 144 6562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196554
X-RAY DIFFRACTIONr_bond_other_d0.0020.025699
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9718929
X-RAY DIFFRACTIONr_angle_other_deg0.952313136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26824.793242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93615921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.211519
X-RAY DIFFRACTIONr_chiral_restr0.0780.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027286
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9725.0053436
X-RAY DIFFRACTIONr_mcbond_other2.9725.0053435
X-RAY DIFFRACTIONr_mcangle_it4.9857.4744262
X-RAY DIFFRACTIONr_mcangle_other4.9847.4744263
X-RAY DIFFRACTIONr_scbond_it2.4034.7643117
X-RAY DIFFRACTIONr_scbond_other2.4024.7653118
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0947.134668
X-RAY DIFFRACTIONr_long_range_B_refined7.07556.7496857
X-RAY DIFFRACTIONr_long_range_B_other7.07556.7536858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194200.08
12B194200.08
21C22220.06
22D22220.06
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 14 -
Rwork0.345 275 -
obs--10.54 %

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