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- PDB-4unu: MCG - a dimer of lambda variable domains -

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Basic information

Entry
Database: PDB / ID: 4unu
TitleMCG - a dimer of lambda variable domains
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: 0.95 Å
AuthorsBrumshtein, B. / Esswein, S.R. / Landau, M. / Ryan, C. / Whitelegge, J. / Casio, 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 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9496
Polymers23,1312
Non-polymers1,8184
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-41.1 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.340, 34.120, 63.180
Angle α, β, γ (deg.)90.00, 104.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11565.510 Da / Num. of mol.: 2 / Fragment: LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110
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-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 373 / 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: 1.8 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growpH: 8 / Details: 2M NACL, 2M (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: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 0.95→40 Å / Num. obs: 89567 / % possible obs: 88 % / Observed criterion σ(I): 3 / Redundancy: 12 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.9 / % possible all: 34

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MCG

3mcg


Resolution: 0.95→39.94 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.454 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.12996 4714 5 %RANDOM
Rwork0.10731 ---
obs0.10846 89567 87.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.976 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.02 Å2
2--0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 0.95→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 41 373 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021781
X-RAY DIFFRACTIONr_bond_other_d0.0010.021574
X-RAY DIFFRACTIONr_angle_refined_deg2.2911.9672456
X-RAY DIFFRACTIONr_angle_other_deg1.1463.0023677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79224.92567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.17154
X-RAY DIFFRACTIONr_chiral_restr0.1660.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212099
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02397
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_it1.1730.664917
X-RAY DIFFRACTIONr_mcbond_other1.1730.664916
X-RAY DIFFRACTIONr_mcangle_it1.4411.0081154
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6730.892864
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_restr7.39333353
X-RAY DIFFRACTIONr_sphericity_free69.667548
X-RAY DIFFRACTIONr_sphericity_bonded16.85453620
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 135 -
Rwork0.219 2576 -
obs--34.08 %

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