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- PDB-6bn0: Avirulence protein 4 (Avr4) from Cladosporium fulvum bound to the... -

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Basic information

Entry
Database: PDB / ID: 6bn0
TitleAvirulence protein 4 (Avr4) from Cladosporium fulvum bound to the hexasaccharide of chitin
ComponentsRace-specific elicitor A4
KeywordsSUGAR BINDING PROTEIN / Plant immunity / effector protein / chitin binding protein / CBM14
Function / homology
Function and homology information


PAMP receptor decoy activity / effector-mediated suppression of host innate immune response / chitin binding / : / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily
Similarity search - Domain/homology
Race-specific elicitor A4
Similarity search - Component
Biological speciesPassalora fulva (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHurlburt, N.K. / Fisher, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007377 United States
CitationJournal: PLoS Pathog. / Year: 2018
Title: Structure of the Cladosporium fulvum Avr4 effector in complex with (GlcNAc)6 reveals the ligand-binding mechanism and uncouples its intrinsic function from recognition by the Cf-4 resistance protein.
Authors: Hurlburt, N.K. / Chen, L.H. / Stergiopoulos, I. / Fisher, A.J.
History
DepositionNov 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 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 / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...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
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: Race-specific elicitor A4
B: Race-specific elicitor A4
C: Race-specific elicitor A4
D: Race-specific elicitor A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,32010
Polymers35,3014
Non-polymers5,0206
Water4,071226
1
A: Race-specific elicitor A4
B: Race-specific elicitor A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1966
Polymers17,6502
Non-polymers2,5454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Race-specific elicitor A4
D: Race-specific elicitor A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1254
Polymers17,6502
Non-polymers2,4742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.864, 41.081, 121.365
Angle α, β, γ (deg.)90.000, 97.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Race-specific elicitor A4


Mass: 8825.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Passalora fulva (fungus) / Gene: AVR4 / Plasmid: pCDG-duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B / References: UniProt: Q00363
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris:HCl, pH 8.5, 30% PEG 4000, 0.8 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.95→60.111 Å / Num. obs: 28654 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.646 % / Biso Wilson estimate: 31.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Χ2: 0.99 / Net I/σ(I): 13.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-23.720.6122.1221100.7480.71699.8
2-2.063.6820.4522.8120540.8370.52899.9
2.06-2.123.430.3593.3219990.8850.42499.8
2.12-2.183.5620.2784.2519280.940.32799.9
2.18-2.253.7910.225.6318660.9540.25799.7
2.25-2.333.8170.2026.1618350.9640.235100
2.33-2.423.7920.1547.917560.9760.17999.7
2.42-2.523.7710.1239.8616830.9840.14399.6
2.52-2.633.6420.10610.7616210.9890.12499.7
2.63-2.763.5150.08812.515460.990.10499.5
2.76-2.913.6560.07115.1414810.9940.08499.7
2.91-3.083.8350.06217.9314270.9960.07299.8
3.08-3.33.7260.04822.9113080.9970.05699.9
3.3-3.563.6610.0428.0612300.9970.04799.3
3.56-3.93.2970.03430.5511170.9980.0498.7
3.9-4.363.4550.02834.3810420.9990.03399.5
4.36-5.043.6730.02637.789140.9990.0399.1
5.04-6.173.570.02834.677680.9990.03398.2
6.17-8.723.2380.02533.986090.9990.0398.7
8.72-60.1113.5690.02338.193600.9990.02798.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z4A

4z4a


Resolution: 1.95→60.111 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.214 1436 5.01 %
Rwork0.1677 --
obs0.1698 28641 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.19 Å2 / Biso mean: 44.4408 Å2 / Biso min: 17.77 Å2
Refinement stepCycle: final / Resolution: 1.95→60.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 342 226 2975
Biso mean--37.97 44.94 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132877
X-RAY DIFFRACTIONf_angle_d1.2613989
X-RAY DIFFRACTIONf_chiral_restr0.066488
X-RAY DIFFRACTIONf_plane_restr0.01477
X-RAY DIFFRACTIONf_dihedral_angle_d12.8411764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.01970.26431130.245327192832100
2.0197-2.10060.29311710.217626942865100
2.1006-2.19620.22171490.197426942843100
2.1962-2.3120.22891570.177426812838100
2.312-2.45680.24131440.170727062850100
2.4568-2.64650.23381660.170126912857100
2.6465-2.91280.22471380.175627272865100
2.9128-3.33430.23281520.165827432895100
3.3343-4.20070.17991230.14492731285499
4.2007-60.13950.18571230.16072819294298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.26160.1961-1.37128.08992.98586.88260.08680.147-0.1605-0.0598-0.094-0.3970.19890.36530.070.40430.02670.0160.21170.00170.33858.2328-12.2953-36.6156
24.091-5.02090.48416.1262-0.8588.5188-0.21830.4269-0.0620.6076-0.0807-0.8250.86330.640.27140.28490.02330.01110.34-0.02840.31455.6857-7.2012-46.4152
34.363-3.7793-2.64469.54172.70015.68-0.2392-0.22410.32121.26840.3807-0.23160.22770.10960.15750.4099-0.0579-0.02090.220.00820.30232.4961-0.6494-31.7171
46.0799-1.84680.1739.3263-0.11664.13620.05740.196-0.56780.4422-0.3445-0.50550.62650.52470.05080.27480.0333-0.05810.24260.08930.323511.4876-6.022-38.3587
53.02381.46420.31245.8720.10495.55760.1446-0.06060.07880.5316-0.20170.32290.0249-0.49590.0720.2524-0.03750.040.2454-0.00240.3263-5.69923.3269-36.3058
67.4751-1.60160.66515.3934-3.68192.55140.0510.7730.492-0.5706-0.6169-0.3164-0.16590.75490.20450.22520.03350.04580.36780.14130.388214.34079.8357-59.7485
73.9982-0.6913-1.3184.7347-1.36763.6190.0111-0.0325-0.0417-0.0869-0.1514-0.32020.0750.17350.14510.140.00760.02120.19690.03790.2755.26517.4938-56.524
80.8788-0.4221-1.71045.353-0.85753.340.13020.04760.1-0.3201-0.10370.168-0.0492-0.1298-0.06120.151-0.0102-0.04130.2157-0.03480.2332-0.01549.3322-57.4857
92.3561-0.7406-0.91638.97913.36157.03960.0431-0.29720.04880.5643-0.4795-0.0989-0.38660.27170.32430.6227-0.0942-0.04930.29020.02660.31966.1332.3664-22.5728
104.75221.67591.07364.36990.70662.99020.1559-0.3817-0.00750.4967-0.1315-0.2948-0.5860.2274-0.07720.5634-0.0477-0.00120.28550.04680.2732.801723.545-21.6256
117.99711.83770.15257.97721.44853.63250.1701-0.57130.94060.1814-0.423-0.831-0.77230.66710.14730.6875-0.1597-0.10960.36810.03960.477410.671228.0524-19.4225
124.0845-0.8135-0.75955.31810.27565.44830.1249-0.1060.10020.6433-0.32970.3493-0.0426-0.73320.20410.3536-0.01480.04140.3006-0.05150.3054-7.108716.6278-26.6377
134.93121.1619-0.08443.21571.39498.81530.1793-0.4439-0.50591.1671-0.5455-0.50151.31560.55410.27340.89680.0122-0.08060.47360.08460.54735.226410.4672-3.7871
145.55982.02361.20675.0658-0.0863.9056-0.0729-0.3282-0.07240.852-0.1053-0.1750.15140.14790.12670.83920.00940.06330.396-0.0080.3281-0.931415.4243-1.1087
153.6055-0.70622.89917.4512-3.84686.5799-0.0753-0.0041-0.37610.61550.36130.92410.6103-0.8078-0.37020.7538-0.08420.14150.4665-0.02950.5738-13.5047.3632-6.0809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 48 )A35 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 56 )A49 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 65 )A57 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 85 )A66 - 85
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 113 )A86 - 113
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 48 )B35 - 48
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 72 )B49 - 72
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 111 )B73 - 111
9X-RAY DIFFRACTION9chain 'C' and (resid 35 through 48 )C35 - 48
10X-RAY DIFFRACTION10chain 'C' and (resid 49 through 72 )C49 - 72
11X-RAY DIFFRACTION11chain 'C' and (resid 73 through 85 )C73 - 85
12X-RAY DIFFRACTION12chain 'C' and (resid 86 through 113 )C86 - 113
13X-RAY DIFFRACTION13chain 'D' and (resid 36 through 56 )D36 - 56
14X-RAY DIFFRACTION14chain 'D' and (resid 57 through 85 )D57 - 85
15X-RAY DIFFRACTION15chain 'D' and (resid 86 through 111 )D86 - 111

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