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- PDB-9cj0: The High-Resolution Structure of a Variable Lymphocyte Receptor f... -

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Basic information

Entry
Database: PDB / ID: 9cj0
TitleThe High-Resolution Structure of a Variable Lymphocyte Receptor from Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix
ComponentsVariable Lymphocyte Receptor
KeywordsIMMUNE SYSTEM / adaptive immune system of jawless vertebrates / alternative antigen receptor / leucine-rich repeat / variable lymphocyte receptor / VLR technologies
Function / homologyChem-EP1
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAppelt, E.A. / Thoden, J.B. / Shusta, E.V. / Holden, H.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM135066 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS099158 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS118028 United States
CitationJournal: Proteins / Year: 2025
Title: The High-Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix.
Authors: Appelt, E.A. / Thoden, J.B. / Gehrke, S.A. / Bachmeier, H.D. / Rayment, I. / Shusta, E.V. / Holden, H.M.
History
DepositionJul 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Dec 11, 2024Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variable Lymphocyte Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1934
Polymers18,7481
Non-polymers4443
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.522, 53.137, 60.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Variable Lymphocyte Receptor


Mass: 18748.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express
#2: Chemical ChemComp-EP1 / 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID


Mass: 252.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.5-2.8 M ammonium sulfate, 2% hexyleneglycol, 100 mM HEPPS (pH 8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. obs: 36207 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 8.1 % / Rsym value: 0.051 / Net I/σ(I): 20.1
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 6984 / Rsym value: 0.42 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.222 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22175 1720 4.8 %RANDOM
Rwork0.18465 ---
obs0.18634 34487 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 26 179 1520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131431
X-RAY DIFFRACTIONr_bond_other_d00.0151360
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6391969
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5773160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44522.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92815244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.776157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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_it1.7661.504699
X-RAY DIFFRACTIONr_mcbond_other1.7621.497698
X-RAY DIFFRACTIONr_mcangle_it2.7192.24877
X-RAY DIFFRACTIONr_mcangle_other2.7182.248878
X-RAY DIFFRACTIONr_scbond_it2.5231.779732
X-RAY DIFFRACTIONr_scbond_other2.4691.753725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8182.5211071
X-RAY DIFFRACTIONr_long_range_B_refined5.59718.7631643
X-RAY DIFFRACTIONr_long_range_B_other5.45518.181600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.331 Å
RfactorNum. reflection% reflection
Rfree0.378 93 -
Rwork0.342 2301 -
obs--89.03 %

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