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- PDB-5uf1: Crystal Structure of Variable Lymphocyte Receptor (VLR) O13 in co... -

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Basic information

Entry
Database: PDB / ID: 5uf1
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) O13 in complex with H-trisaccharide
ComponentsO13
KeywordsIMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor
Function / homologyH type 2 antigen, beta anomer
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsGunn, R.J. / Collins, B.C. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2017
Title: Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates.
Authors: Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _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 / entity_name_com / 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_molecule_features / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: O13
A: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7575
Polymers54,6622
Non-polymers1,0943
Water6,503361
1
B: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8963
Polymers27,3311
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8612
Polymers27,3311
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.124, 78.968, 83.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 22:54 or (resid 55 and (name...
21(chain B and (resseq 22:54 or (resid 55 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSLEULEU(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 547 - 39
12TYRTYRTYRTYR(chain A and (resseq 22:54 or (resid 55 and (name...AB5540
13CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
14CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
15CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
16CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
17CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
18CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
19CYSCYSPROPRO(chain A and (resseq 22:54 or (resid 55 and (name...AB22 - 2627 - 247
21CYSCYSLEULEU(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 547 - 39
22TYRTYRTYRTYR(chain B and (resseq 22:54 or (resid 55 and (name...BA5540
23CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247
24CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247
25CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247
26CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247
27CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247
28CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247
29CYSCYSPROPRO(chain B and (resseq 22:54 or (resid 55 and (name...BA22 - 2627 - 247

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Components

#1: Protein O13


Mass: 27331.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 2 antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 2 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 10 mg/mL O13, 14% PEG6000, 1 M lithium chloride, 0.1 M citrate, pH 5.2, 1.9 mM H-trisaccharide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.03→47.902 Å / Num. obs: 32373 / % possible obs: 85.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.13 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.03-2.12.40.61314660.619139.8
2.1-2.192.80.4640.729157.1
2.19-2.293.20.4170.785173.9
2.29-2.4140.350.877185.2
2.41-2.565.30.2880.944196
2.56-2.767.40.2440.9751100
2.76-3.037.40.1620.991100
3.03-3.477.40.1130.9941100
3.47-4.377.30.0770.9961100
4.37-47.970.0660.9971100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UEI

5uei


Resolution: 2.03→47.902 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.2113 1813 5.61 %
Rwork0.1869 --
obs0.1883 32335 85.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.13 Å2 / Biso mean: 25.4388 Å2 / Biso min: 1.77 Å2
Refinement stepCycle: final / Resolution: 2.03→47.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 73 361 4107
Biso mean--21.97 30.05 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023833
X-RAY DIFFRACTIONf_angle_d0.6195239
X-RAY DIFFRACTIONf_chiral_restr0.039642
X-RAY DIFFRACTIONf_plane_restr0.003660
X-RAY DIFFRACTIONf_dihedral_angle_d10.5132355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2334X-RAY DIFFRACTION5.898TORSIONAL
12B2334X-RAY DIFFRACTION5.898TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.08490.2993650.26661019108438
2.0849-2.14620.2834810.24631385146651
2.1462-2.21550.25761080.23661739184765
2.2155-2.29470.28881270.21772063219076
2.2947-2.38660.24641350.21672299243485
2.3866-2.49520.24831390.20912558269794
2.4952-2.62670.22941300.20852751288199
2.6267-2.79130.23131220.217527702892100
2.7913-3.00670.27621810.206227342915100
3.0067-3.30930.24261610.201327432904100
3.3093-3.7880.20581320.167428222954100
3.788-4.77170.14481670.138327852952100
4.7717-47.91540.17052650.1628543119100
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)
10.9934-0.2391-0.72082.4904-1.02112.53110.08010.2158-0.0025-0.6272-0.2998-0.23550.86020.23070.03790.36140.1231-0.02980.4375-0.12370.3179-15.0062-16.0373-41.9303
21.2421-0.5304-0.44941.37940.17262.05160.07480.1714-0.3209-0.1023-0.00310.03810.36950.1223-0.06510.22530.0104-0.02530.2032-0.04890.2391-25.3742-13.0364-36.7224
31.8951-0.0951-0.41841.42430.3111.5889-0.03620.0223-0.06020.047-0.0149-0.08270.10490.07820.01170.15-0.023-0.00070.1588-0.01180.1497-29.3077-5.4499-25.4256
41.4654-0.6010.05331.49380.51741.2621-0.02360.0104-0.0193-0.01450.0786-0.03240.00520.0075-0.0490.1493-0.0401-0.00480.15390.01120.1456-31.77029.2253-20.4952
52.5126-0.4573-0.51331.25650.31471.28950.01530.19930.118-0.08080.0071-0.0739-0.2152-0.0582-0.01060.1924-0.02530.01690.14810.00920.1624-31.392620.4199-19.5411
62.6267-1.9143-2.15383.14032.06323.9312-0.19570.3503-0.2683-0.1355-0.48980.373-0.5554-0.11540.41830.24260.032-0.06330.34370.10230.2974-32.507135.7689-26.1494
71.64620.23840.66880.68160.29712.1521-0.0730.02030.1702-0.0155-0.02280.0897-0.1078-0.07570.09360.1704-0.0212-0.00850.12160.00890.2001-18.733137.5568-15.3988
82.5536-0.5350.11260.8229-0.58191.43450.0507-0.11910.06920.04250.01850.00190.08190.0564-0.1110.1749-0.0389-0.02030.1691-0.01550.1631-4.165425.1961-4.7406
92.0661-0.08721.18840.761-0.15592.0060.05970.1326-0.2729-0.14980.0748-0.0470.17220.1526-0.13550.21810.0082-0.0190.1539-0.01860.21681.982915.8302-3.7436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 22 through 34 )B22 - 34
2X-RAY DIFFRACTION2chain 'B' and (resid 35 through 94 )B35 - 94
3X-RAY DIFFRACTION3chain 'B' and (resid 95 through 151 )B95 - 151
4X-RAY DIFFRACTION4chain 'B' and (resid 152 through 208 )B152 - 208
5X-RAY DIFFRACTION5chain 'B' and (resid 209 through 262 )B209 - 262
6X-RAY DIFFRACTION6chain 'A' and (resid 22 through 34 )A22 - 34
7X-RAY DIFFRACTION7chain 'A' and (resid 35 through 151 )A35 - 151
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 208 )A152 - 208
9X-RAY DIFFRACTION9chain 'A' and (resid 209 through 262 )A209 - 262

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