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- PDB-4aiz: Crystallographic structure of 3mJL2 from the germinal line lambda 3 -

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Basic information

Entry
Database: PDB / ID: 4aiz
TitleCrystallographic structure of 3mJL2 from the germinal line lambda 3
Components(V2-17 PROTEIN) x 2
KeywordsIMMUNE SYSTEM / AMYLOIDOSIS
Function / homology
Function and homology information


Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade ...Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / 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 / extracellular region
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
Chem-88Q / CITRIC ACID / V2-17 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVillalba, M.I. / Luna, O.D. / Rudino-Pinera, E. / Sanchez, R. / Sanchez-Lopez, R. / Rojas-Trejo, S. / Olamendi-Portugal, T. / Fernandez-Velasco, D.A. / Becerril, B.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Site-Directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human Lambda3R Light Chains.
Authors: Villalba, M.I. / Canul-Tec, J.C. / Luna-Martinez, O.D. / Sanchez-Alcala, R. / Olamendi-Portugal, T. / Rudino-Pinera, E. / Rojas, S. / Sanchez-Lopez, R. / Fernandez-Velasco, D.A. / Becerril, B.
History
DepositionFeb 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V2-17 PROTEIN
B: V2-17 PROTEIN
C: V2-17 PROTEIN
D: V2-17 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7158
Polymers46,0694
Non-polymers6474
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-73.1 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.402, 40.946, 106.726
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules ACDB

#1: Antibody V2-17 PROTEIN / 3MJL2


Mass: 11517.674 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NV90
#2: Antibody V2-17 PROTEIN / 3MJL2


Mass: 11515.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NV90

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Non-polymers , 4 types, 409 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-88Q / 1,5:6,10-dianhydro-3,4,7,8-tetradeoxy-2,9-bis-C-(hydroxymethyl)-L-manno-decitol


Mass: 262.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details88Q WAS CONSTRUCTED BASED ON THE ELECTRON DENSITY IN THE POSITION, HOWEVER WE WERE NOT ABLE TO FIND ...88Q WAS CONSTRUCTED BASED ON THE ELECTRON DENSITY IN THE POSITION, HOWEVER WE WERE NOT ABLE TO FIND THE ORIGIN OF IT.
Sequence detailsTHIS DEPOSIT IS THE FIRST REFERENCE TO THE SEQUENCE OF 3MJL2.

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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: 2.1 Å3/Da / Density % sol: 41.33 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M SODIUM CITRATE, 0.1 M HEPES, 30 % MPD, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 1, 2011
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 31323 / % possible obs: 79.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 17.22 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 74.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIL

1lil


Resolution: 1.75→34.224 Å / SU ML: 0.38 / σ(F): 1.38 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1588 5.1 %
Rwork0.1662 --
obs0.1689 31297 79.46 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.115 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.2972 Å20 Å20.0109 Å2
2--0.8386 Å20 Å2
3----1.1357 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 41 405 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.033474
X-RAY DIFFRACTIONf_angle_d2.0564752
X-RAY DIFFRACTIONf_dihedral_angle_d14.681286
X-RAY DIFFRACTIONf_chiral_restr0.146514
X-RAY DIFFRACTIONf_plane_restr0.006627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.29231190.20282514X-RAY DIFFRACTION74
1.8065-1.87110.28041130.19192507X-RAY DIFFRACTION74
1.8711-1.9460.23741450.18952467X-RAY DIFFRACTION73
1.946-2.03450.25941300.18542479X-RAY DIFFRACTION73
2.0345-2.14180.22561330.18232491X-RAY DIFFRACTION74
2.1418-2.27590.24331390.17332495X-RAY DIFFRACTION74
2.2759-2.45160.24761420.18232493X-RAY DIFFRACTION74
2.4516-2.69820.25821370.18212609X-RAY DIFFRACTION77
2.6982-3.08850.24051720.17412920X-RAY DIFFRACTION86
3.0885-3.89030.18571720.14133287X-RAY DIFFRACTION96
3.8903-34.23010.17681860.1513447X-RAY DIFFRACTION97

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