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- PDB-2agj: Crystal Structure of a glycosylated Fab from an IgM cryoglobulin ... -

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Basic information

Entry
Database: PDB / ID: 2agj
TitleCrystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody
Components
  • Yvo Fab, Heavy Chain
  • Yvo Fab, Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin superfamily / catalytic antibody
Function / homology
Function and homology information


hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / IgM immunoglobulin complex / CD22 mediated BCR regulation / immunoglobulin complex / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall ...hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / pre-B cell allelic exclusion / IgM immunoglobulin complex / CD22 mediated BCR regulation / immunoglobulin complex / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / antibacterial humoral response / defense response to Gram-negative bacterium / blood microparticle / Potential therapeutics for SARS / adaptive immune response / innate immune response / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant mu / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRamsland, P.A. / Terzyan, S.S. / Cloud, G. / Bourne, C.R. / Farrugia, W. / Tribbick, G. / Geysen, H.M. / Moomaw, C.R. / Slaughter, C.A. / Edmundson, A.B.
Citation
Journal: Biochem.J. / Year: 2006
Title: Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody
Authors: Ramsland, P.A. / Terzyan, S.S. / Cloud, G. / Bourne, C.R. / Farrugia, W. / Tribbick, G. / Geysen, H.M. / Moomaw, C.R. / Slaughter, C.A. / Edmundson, A.B.
#1: Journal: J.Cryst.Growth / Year: 2001
Title: Interconversion of different crystal forms of Fabs from human IgM cryoglobulins
Authors: Ramsland, P.A. / Upshaw, J.L. / Shultz, B.B. / DeWitt, C.R. / Chissoe III, W.F. / Raison, R.L. / Edmundson, A.B.
#2: Journal: J.Mol.Recog. / Year: 2002
Title: Dealing with intractable protein cores: protein sequencing of the Mcg IgG and the Yvo IgM heavy chain variable domains
Authors: Shaw, D.C. / Shultz, B.B. / Ramsland, P.A. / Edmundson, A.B.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 25, 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
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Yvo Fab, Light Chain
H: Yvo Fab, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3503
Polymers47,9262
Non-polymers4241
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-14 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.433, 103.653, 138.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody Yvo Fab, Light Chain


Mass: 23367.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PJF2
#2: Antibody Yvo Fab, Heavy Chain


Mass: 24557.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01871
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 15000-20000, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 14, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 18260 / Num. obs: 18260 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Biso Wilson estimate: 52.8 Å2 / Rsym value: 0.102 / Net I/σ(I): 32.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 1742 / Rsym value: 0.854 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGM 1DN0

1igm

1dn0


Resolution: 2.6→42.2 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 -RANDOM
Rwork0.219 --
all0.225 --
obs0.225 18260 -
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 28 20 3420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8

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