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- PDB-5ir3: Crystal structure of the recombinant highest fibrillogenic natura... -

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Basic information

Entry
Database: PDB / ID: 5ir3
TitleCrystal structure of the recombinant highest fibrillogenic natural mutant (obtained from patient AR) derived from lambda 6 light chain variable domain
ComponentsIg lambda chain V-VI region AR
KeywordsIMMUNE SYSTEM / BETA-SANDWICH / IMMUNOGLOBULIN / AL AMYLOIDOSIS
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Immunoglobulin lambda variable 6-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHernandez-Santoyo, A. / Rodriguez-Romero, A.
Citation
#1: Journal: J. Mol. Biol. / Year: 2010
Title: A single mutation at the sheet switch region results in conformational changes favoring lambda6 light-chain fibrillogenesis.
Authors: Hernandez-Santoyo, A. / Del Pozo-Yauner, L. / Fuentes-Silva, D. / Ortiz, E. / Rudino-Pinera, E. / Sanchez-Lopez, R. / Horjales, E. / Becerril, B. / Rodriguez-Romero, A.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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
A: Ig lambda chain V-VI region AR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9862
Polymers11,9271
Non-polymers591
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.121, 71.121, 96.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Antibody Ig lambda chain V-VI region AR


Mass: 11926.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSYN1 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 / References: UniProt: P01721
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Sodium cacodylate pH 6.5; 1.4M Sodium acetate / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→34.81 Å / Num. obs: 13830 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(DEV_2313)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B5G

3b5g


Resolution: 1.7→34.81 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.25 / Phase error: 20.79
RfactorNum. reflection% reflectionSelection details
Rfree0.207 651 4.71 %RANDOM
Rwork0.174 ---
obs0.176 13829 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 4 156 994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006918
X-RAY DIFFRACTIONf_angle_d0.9711267
X-RAY DIFFRACTIONf_dihedral_angle_d17.451340
X-RAY DIFFRACTIONf_chiral_restr0.098140
X-RAY DIFFRACTIONf_plane_restr0.006170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7003-1.83160.27821350.24132587X-RAY DIFFRACTION100
1.8316-2.01590.22171330.19912598X-RAY DIFFRACTION99
2.0159-2.30760.25191280.17462618X-RAY DIFFRACTION100
2.3076-2.90710.20791270.17322656X-RAY DIFFRACTION100
2.9071-34.81530.17081280.15282719X-RAY DIFFRACTION97

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