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- PDB-7lur: Stable Effector Functionless 2 (SEFL2) IgG1 Fc Scaffold Bound to ... -

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Basic information

Entry
Database: PDB / ID: 7lur
TitleStable Effector Functionless 2 (SEFL2) IgG1 Fc Scaffold Bound to a Minimized Version of the B-domain (Mini-Z) from Protein A Called Z34C
Components
  • Immunoglobulin heavy constant gamma 1
  • Mini Z domain
KeywordsIMMUNE SYSTEM / fragment crystallizable / Fc
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
Model detailsFc
AuthorsSudom, A. / Garces, F. / Wang, Z.
CitationJournal: Iscience / Year: 2021
Title: Next generation Fc scaffold for multispecific antibodies.
Authors: Estes, B. / Sudom, A. / Gong, D. / Whittington, D.A. / Li, V. / Mohr, C. / Li, D. / Riley, T.P. / Shi, S.D. / Zhang, J. / Garces, F. / Wang, Z.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy constant gamma 1
B: Immunoglobulin heavy constant gamma 1
C: Mini Z domain
D: Mini Z domain


Theoretical massNumber of molelcules
Total (without water)59,3934
Polymers59,3934
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-27 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.438, 69.335, 135.421
Angle α, β, γ (deg.)90.000, 98.640, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Immunoglobulin heavy constant gamma 1 / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma- ...Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE


Mass: 25505.928 Da / Num. of mol.: 2 / Mutation: N297G, R292C, V302C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Protein/peptide Mini Z domain


Mass: 4190.682 Da / Num. of mol.: 2 / Fragment: Mini Z domain Z34C / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.48 Å3/Da / Density % sol: 50.38 % / Mosaicity: 0.25 °
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M ammonium tartrate, 20% (w/v) PEG 3350, 10% NDSB-221

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.51 Å / Num. obs: 42098 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.246 / Net I/σ(I): 6.9 / Num. measured all: 283884
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-26.91.8972037729320.4781.398.5
8.94-46.516.60.0830654670.99122.798.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6X

1l6x


Resolution: 1.95→40.36 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 2104 5 %
Rwork0.2158 39975 -
obs0.218 42079 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.02 Å2 / Biso mean: 28.5066 Å2 / Biso min: 11.35 Å2
Refinement stepCycle: final / Resolution: 1.95→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 0 212 4092
Biso mean---26.98 -
Num. residues----482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.36591340.30252630276498
2-2.050.29471290.2762625275498
2.05-2.10.31981470.2662665281299
2.1-2.160.29171370.25072615275299
2.16-2.230.33151460.28152658280499
2.23-2.310.37411490.33932635278498
2.31-2.40.29781490.2512622277199
2.4-2.510.28051400.23262649278999
2.51-2.650.28881390.22532671281099
2.65-2.810.26811400.2242656279699
2.81-3.030.25151280.22132704283299
3.03-3.330.26661390.214126832822100
3.33-3.820.28171270.188326962823100
3.82-4.810.17121400.155627152855100
4.81-40.360.19631600.166827512911100

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