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- PDB-4unt: Induced monomer of the Mcg variable domain -

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Basic information

Entry
Database: PDB / ID: 4unt
TitleInduced monomer of the Mcg variable domain
ComponentsIG LAMBDA CHAIN V-II REGION MGC
KeywordsIMMUNE SYSTEM / BENCE-JONES / LIGHT CHAINS / IMMUNOGLOBULIN / AMYLOID
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 space / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBrumshtein, B. / Esswein, S.R. / Landau, M. / Ryan, C.M. / Whitelegge, J.P. / Phillips, M.L. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Formation of Amyloid Fibers by Monomeric Light-Chain Variable Domains.
Authors: Brumshtein, B. / Esswein, S.R. / Landau, M. / Ryan, C.M. / Whitelegge, J.P. / Phillips, M.L. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
History
DepositionMay 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IG LAMBDA CHAIN V-II REGION MGC
B: IG LAMBDA CHAIN V-II REGION MGC
C: IG LAMBDA CHAIN V-II REGION MGC
D: IG LAMBDA CHAIN V-II REGION MGC
E: IG LAMBDA CHAIN V-II REGION MGC
F: IG LAMBDA CHAIN V-II REGION MGC
G: IG LAMBDA CHAIN V-II REGION MGC
H: IG LAMBDA CHAIN V-II REGION MGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,74721
Polymers91,4988
Non-polymers1,24913
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25530 Å2
ΔGint-109.4 kcal/mol
Surface area43740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.130, 90.350, 99.170
Angle α, β, γ (deg.)90.00, 118.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
IG LAMBDA CHAIN V-II REGION MGC / MCG-MONOMER


Mass: 11437.292 Da / Num. of mol.: 8 / Fragment: LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01709
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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 % / Description: NONE
Crystal growpH: 8 / Details: 0.5M LICL, 1.65M (NH4)2SO4, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: PILATUS PILATUS / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→65 Å / Num. obs: 20681 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MCG

3mcg


Resolution: 2.7→63.88 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.815 / SU B: 15.968 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28925 1089 5 %RANDOM
Rwork0.24328 ---
obs0.24557 20681 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.57 Å2
2---0.32 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→63.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6206 0 65 57 6328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026427
X-RAY DIFFRACTIONr_bond_other_d0.0070.025597
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.968766
X-RAY DIFFRACTIONr_angle_other_deg1.274312986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18425.72243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69415924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3341516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217496
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021344
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_it1.9643.1263478
X-RAY DIFFRACTIONr_mcbond_other1.9643.1253477
X-RAY DIFFRACTIONr_mcangle_it3.2164.6824333
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1223.272949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 80 -
Rwork0.314 1522 -
obs--99.56 %

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