PDB-6grf: Crystal structure of the tandem DUF26 ectodomain from the Arabido...

ID or keywords:

Entry

Database: PDB / ID: 6grf

Title

Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP8.

Components

Cysteine-rich repeat secretory protein 15

Keywords

SIGNALING PROTEIN / lectin / membrane protein / DUF26 domain / disulfide bond / plasmodesmata / immune signaling

Function / homology

Gnk2-homologous domain / Gnk2-homologous domain superfamily / Salt stress response/antifungal / Gnk2-homologous domain profile. / plasmodesma / viral process / membrane => GO:0016020 / plasma membrane / Plasmodesmata-located protein 8

Function and homology information

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Brandt, B. / Hothorn, M.

Funding support

Switzerland, 1items

Citation

Journal: Commun Biol / Year: 2019
Title: Mechanistic insights into the evolution of DUF26-containing proteins in land plants.
Authors: Vaattovaara, A. / Brandt, B. / Rajaraman, S. / Safronov, O. / Veidenberg, A. / Luklova, M. / Kangasjarvi, J. / Loytynoja, A. / Hothorn, M. / Salojarvi, J. / Wrzaczek, M.

History

Deposition	Jun 11, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Jan 17, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6grf.cif.gz	256.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6grf.ent.gz	209.4 KB	Display	PDB format
PDBx/mmJSON format	6grf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6grf_validation.pdf.gz	477 KB	Display	wwPDB validaton report
Full document	6grf_full_validation.pdf.gz	485.2 KB	Display
Data in XML	6grf_validation.xml.gz	25.5 KB	Display
Data in CIF	6grf_validation.cif.gz	35.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/6grf ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6grf	HTTPS FTP

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Related structure data

Related structure data	6greSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6gre-1 3szm-4 1cdc-d 1qwi-1 3vqm-6 2i32-2 1qwi-2 3szm-6 3shv-1 1a7m-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6greSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cysteine-rich repeat secretory protein 15

B: Cysteine-rich repeat secretory protein 15

C: Cysteine-rich repeat secretory protein 15

hetero molecules

79.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cysteine-rich repeat secretory protein 15

hetero molecules

defined by author
Evidence: gel filtration
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cysteine-rich repeat secretory protein 15

hetero molecules

defined by author
26.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Cysteine-rich repeat secretory protein 15

defined by author
26.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	143.862, 143.862, 59.722
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-403- HOH
2	1	A-408- HOH
3	1	A-432- HOH
4	1	A-460- HOH
5	1	A-468- HOH

#1: Protein

Cysteine-rich repeat secretory protein 15 / Plasmodesmata-located protein 8 / PDLP8

Mass: 26438.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: CRRSP15, At3g60720, T4C21_130 / Plasmid: pFastBac1 / Cell line (production host): Tnao / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: Q6NKQ9

#2: 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

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.32 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17.5 % polyethylene glycol 4,000, 0.1 M citrate pH 5.5, 20 % (v/v) 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999871 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 19, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999871 Å / Relative weight: 1
Reflection	Resolution: 1.95→20.1 Å / Num. obs: 51859 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.3 % / CC_1/2: 0.998 / R_rim(I) all: 0.32 / R_sym value: 0.31 / Net I/σ(I): 8.82
Reflection shell	Resolution: 1.95→2.07 Å / Redundancy: 19.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 8245 / CC_1/2: 0.647 / R_rim(I) all: 3.62 / R_sym value: 3.52 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6GRE

6gre

Resolution: 1.95→20.1 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.945 / SU B: 15.364 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26189	2591	5 %	RANDOM
R_work	0.2285	-	-	-
obs	0.23018	49227	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.671 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.56 Å²	0.28 Å²	0 Å²
2-	-	0.56 Å²	-0 Å²
3-	-	-	-1.82 Å²

Refinement step

Cycle: 1 / Resolution: 1.95→20.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4791	0	28	193	5012

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.014	4966
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4187
X-RAY DIFFRACTION	r_angle_refined_deg	1.148	1.658	6735
X-RAY DIFFRACTION	r_angle_other_deg	0.845	1.657	9872
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.776	5	634
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.346	22.48	250
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.328	15	799
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.392	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	641
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5684
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	976
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.926	2.498	2515
X-RAY DIFFRACTION	r_mcbond_other	0.926	2.498	2514
X-RAY DIFFRACTION	r_mcangle_it	1.619	3.737	3138
X-RAY DIFFRACTION	r_mcangle_other	1.618	3.737	3139
X-RAY DIFFRACTION	r_scbond_it	1.063	2.643	2451
X-RAY DIFFRACTION	r_scbond_other	1.063	2.643	2452
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.756	3.922	3592
X-RAY DIFFRACTION	r_long_range_B_refined	4.154	29.424	5466
X-RAY DIFFRACTION	r_long_range_B_other	4.122	29.174	5427
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	188	-
R_work	0.398	3576	-
obs	-	-	99.87 %

Refinement TLS params.

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

ID	L11 (°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)
1	1.6414	1.4409	0.2503	2.7907	-3.2804	8.7002	0.0176	-0.0144	0.1734	0.1716	-0.0218	0.1089	-0.5733	0.3229	0.0043	0.2389	-0.0632	-0.0028	0.2084	-0.0161	0.1086	28.5365	16.2924	6.1849
2	2.6383	2.1705	1.1947	6.4943	1.5978	7.4239	0.0297	-0.1351	-0.0092	0.1625	0.0571	0.0051	-0.0015	0.2359	-0.0867	0.059	-0.0175	-0.0247	0.1645	0.0522	0.0285	28.1118	3.6723	7.0125
3	4.3924	1.8611	-2.039	6.0901	-1.6931	4.51	0.1043	0.2622	-0.1474	-0.2532	0.0701	-0.6535	-0.2476	0.3591	-0.1744	0.0911	-0.041	0.0294	0.2579	-0.005	0.1229	31.696	7.9401	-1.1775
4	0.9809	-0.0822	0.6009	0.8965	-0.161	3.9638	-0.0872	0.0095	0.1165	0.0134	0.002	0.0418	-0.3369	0.0057	0.0852	0.0866	-0.0291	-0.0165	0.1612	0.0238	0.0201	19.1375	12.4719	-13.827
5	4.8113	-2.0094	-3.1942	7.136	-1.363	6.335	-0.1843	0.1012	0.0536	-0.3389	-0.0018	-0.4643	0.1719	0.4929	0.1861	0.1306	-0.0558	-0.0438	0.2138	0.0019	0.1264	25.2616	15.0635	-25.2517
6	5.216	-0.1776	-1.1195	1.8709	1.3365	4.0911	0.0013	0.2386	-0.0862	0.0163	0.0488	0.2574	-0.0119	-0.3709	-0.0501	0.172	-0.048	0.0153	0.1384	0.0039	0.0679	49.5271	20.5426	-6.6905
7	0.0416	0.2524	-0.4031	1.5955	-2.5343	4.0327	0.0091	-0.0114	0.0146	0.0728	-0.0864	-0.0718	-0.1459	0.1167	0.0773	0.3459	-0.0044	0.0019	0.3123	-0.0055	0.4305	53.9614	30.0483	-18.5658
8	5.4768	0.7211	-1.3467	3.9456	-1.2229	2.8429	0.0952	-0.2938	-0.499	0.2462	0.0028	-0.1073	0.4312	-0.0225	-0.098	0.1995	-0.0807	-0.0172	0.1675	-0.0349	0.1132	52.067	16.4489	1.2981
9	0.9564	-0.0143	0.119	1.2639	1.1339	4.0911	-0.0002	0.0133	0.0977	-0.022	-0.0481	0.1247	-0.1303	-0.3663	0.0482	0.1432	-0.0428	0.0251	0.1692	0.0069	0.0466	50.3571	28.7172	11.9136
10	6.9018	-0.2473	-3.8585	1.1691	0.9242	5.5428	-0.0239	-0.033	0.0731	-0.1728	-0.0951	0.0838	-0.1596	-0.1441	0.119	0.1383	-0.0157	-0.0136	0.0962	-0.0066	0.0217	52.8627	31.938	13.8923
11	3.5075	0.6501	1.7628	0.5144	1.5217	7.9707	0.0982	-0.2342	-0.1652	0.1434	-0.1311	0.1717	0.1531	-0.6257	0.0328	0.2533	0.0138	0.0065	0.241	-0.0402	0.233	43.3552	56.5243	6.0477
12	7.6404	-0.8457	-0.0488	3.2897	1.475	5.989	0.0579	-0.0727	0.1244	0.2081	0.0723	-0.0341	-0.2432	-0.3297	-0.1302	0.1863	0.0127	-0.0304	0.0885	-0.051	0.0759	54.6069	64.0456	5.2191
13	6.3828	0.0143	2.1222	4.716	-1.0715	4.8838	0.1745	0.1231	0.4479	-0.0546	-0.0674	0.482	-0.2041	-0.4105	-0.1072	0.2015	0.0609	0.0059	0.1747	-0.0387	0.1148	47.3953	61.7185	-1.1492
14	1.0225	0.4813	0.3492	1.7967	0.7703	3.9643	-0.0014	0.0967	-0.1262	-0.0615	0.0008	0.081	0.1493	-0.1957	0.0006	0.1403	0.0455	-0.0043	0.131	-0.0161	0.0613	51.667	50.7001	-19.3058
15	4.8958	0.6084	3.4022	1.4576	1.5353	5.6192	-0.0591	0.0041	-0.0197	0.0767	-0.0984	0.1211	0.0812	-0.1338	0.1575	0.1633	0.0253	0.0172	0.1183	-0.0124	0.0138	52.324	49.7269	-15.7615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 48
2	X-RAY DIFFRACTION	2	A	49 - 79
3	X-RAY DIFFRACTION	3	A	80 - 113
4	X-RAY DIFFRACTION	4	A	114 - 230
5	X-RAY DIFFRACTION	5	A	231 - 237
6	X-RAY DIFFRACTION	6	B	26 - 70
7	X-RAY DIFFRACTION	7	B	71 - 79
8	X-RAY DIFFRACTION	8	B	80 - 108
9	X-RAY DIFFRACTION	9	B	109 - 189
10	X-RAY DIFFRACTION	10	B	190 - 236
11	X-RAY DIFFRACTION	11	C	26 - 49
12	X-RAY DIFFRACTION	12	C	50 - 74
13	X-RAY DIFFRACTION	13	C	80 - 130
14	X-RAY DIFFRACTION	14	C	131 - 189
15	X-RAY DIFFRACTION	15	C	190 - 236

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