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- PDB-6qwn: Protein peptide complex -

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Basic information

Entry
Database: PDB / ID: 6qwn
TitleProtein peptide complex
Components
  • Pollen-specific leucine-rich repeat extensin-like protein 1
  • Protein RALF-like 4
KeywordsPLANT PROTEIN / Leucine rich extensin / peptide signaling / cell wall signaling / LRR
Function / homology
Function and homology information


regulation of pollen tube growth / pollen tube growth / structural constituent of cell wall / apoplast / calcium-mediated signaling / cell wall organization / hormone activity / cell-cell signaling / extracellular region
Similarity search - Function
Rapid ALkalinization Factor / Rapid ALkalinization Factor (RALF) / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Protein RALF-like 4 / Pollen-specific leucine-rich repeat extensin-like protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.892 Å
AuthorsMoussu, S. / Caroline, C. / Santos-Fernandez, G. / Wehrle, S. / Grossniklaus, U. / Santiago, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council716358 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth.
Authors: Moussu, S. / Broyart, C. / Santos-Fernandez, G. / Augustin, S. / Wehrle, S. / Grossniklaus, U. / Santiago, J.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pollen-specific leucine-rich repeat extensin-like protein 1
F: Protein RALF-like 4
B: Pollen-specific leucine-rich repeat extensin-like protein 1
G: Protein RALF-like 4
C: Pollen-specific leucine-rich repeat extensin-like protein 1
H: Protein RALF-like 4
D: Pollen-specific leucine-rich repeat extensin-like protein 1
I: Protein RALF-like 4
E: Pollen-specific leucine-rich repeat extensin-like protein 1
J: Protein RALF-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,35318
Polymers242,91910
Non-polymers3,4348
Water0
1
A: Pollen-specific leucine-rich repeat extensin-like protein 1
F: Protein RALF-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5544
Polymers48,5842
Non-polymers9702
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-4 kcal/mol
Surface area18250 Å2
MethodPISA
2
B: Pollen-specific leucine-rich repeat extensin-like protein 1
G: Protein RALF-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5954
Polymers48,5842
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint0 kcal/mol
Surface area18660 Å2
MethodPISA
3
C: Pollen-specific leucine-rich repeat extensin-like protein 1
H: Protein RALF-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5954
Polymers48,5842
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint2 kcal/mol
Surface area19060 Å2
MethodPISA
4
D: Pollen-specific leucine-rich repeat extensin-like protein 1
I: Protein RALF-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0264
Polymers48,5842
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-8 kcal/mol
Surface area17920 Å2
MethodPISA
5
E: Pollen-specific leucine-rich repeat extensin-like protein 1
J: Protein RALF-like 4


Theoretical massNumber of molelcules
Total (without water)48,5842
Polymers48,5842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-14 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.841, 114.091, 146.977
Angle α, β, γ (deg.)90.00, 116.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
Pollen-specific leucine-rich repeat extensin-like protein 1 / Pollen-specific LRR/EXTENSIN1 / Cell wall hydroxyproline-rich glycoprotein


Mass: 41765.914 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: pollen / Cell: pollen / Gene: PEX1, At3g19020, K13E13.23 / Plasmid: pACEBac1 / Cell (production host): pollen / Cell line (production host): TNAO38 / Organ (production host): pollen / Production host: Trichoplusia ni (cabbage looper) / Tissue (production host): pollen / References: UniProt: Q9LJ64
#2: Protein
Protein RALF-like 4


Mass: 6817.940 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: pollen / Cell: pollen / Gene: RALFL4, At1g28270, F3H9.8 / Plasmid: pACEBac1 / Cell (production host): pollen / Cell line (production host): TNAO38 / Organ (production host): pollen / Production host: Trichoplusia ni (cabbage looper) / Tissue (production host): pollen / References: UniProt: Q9FZA0

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Sugars , 6 types, 8 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a6-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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 genetically manipulated 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)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.34 % / Description: Elongated three dimensional needle
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 17.5% (w/v) PEG 8000, 0.1 M Bis-Tris pH7, 0.2 M sodium citrate
PH range: ph 7

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999871 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 27, 2018
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999871 Å / Relative weight: 1
ReflectionResolution: 3.892→49.44 Å / Num. obs: 28176 / % possible obs: 99.6 % / Observed criterion σ(I): 0.95 / Redundancy: 6.7 % / Biso Wilson estimate: 110.49 Å2 / CC1/2: 0.978 / Rrim(I) all: 0.495 / Rsym value: 0.457 / Net I/σ(I): 4.44
Reflection shellResolution: 3.892→4.13 Å / Redundancy: 6.71 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 4482 / CC1/2: 0.34 / Rrim(I) all: 2.26 / Rsym value: 2.092 / % possible all: 99.2

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LRX2

Resolution: 3.892→49.44 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.68
RfactorNum. reflection% reflection
Rfree0.3292 1407 5 %
Rwork0.2816 --
obs0.284 28124 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.892→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14844 0 226 0 15070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315467
X-RAY DIFFRACTIONf_angle_d0.75620966
X-RAY DIFFRACTIONf_dihedral_angle_d7.9859292
X-RAY DIFFRACTIONf_chiral_restr0.0492275
X-RAY DIFFRACTIONf_plane_restr0.0052734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8916-4.03060.37931370.32662604X-RAY DIFFRACTION98
4.0306-4.19190.34921400.3172669X-RAY DIFFRACTION100
4.1919-4.38260.34821400.30442648X-RAY DIFFRACTION100
4.3826-4.61350.34761390.28112648X-RAY DIFFRACTION100
4.6135-4.90230.32111420.27322703X-RAY DIFFRACTION100
4.9023-5.28040.31551390.28022633X-RAY DIFFRACTION100
5.2804-5.8110.3631410.29762682X-RAY DIFFRACTION100
5.811-6.65020.35581420.29972691X-RAY DIFFRACTION100
6.6502-8.37190.34771410.28012689X-RAY DIFFRACTION100
8.3719-49.46020.27631460.24612750X-RAY DIFFRACTION100

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