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- PDB-1l6x: FC FRAGMENT OF RITUXIMAB BOUND TO A MINIMIZED VERSION OF THE B-DO... -

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Basic information

Entry
Database: PDB / ID: 1l6x
TitleFC FRAGMENT OF RITUXIMAB BOUND TO A MINIMIZED VERSION OF THE B-DOMAIN FROM PROTEIN A CALLED Z34C
Components
  • IMMUNOGLOBULIN GAMMA-1 HEAVY CHAIN CONSTANT REGION
  • Minimized B-domain of Protein A Z34C
KeywordsIMMUNE SYSTEM / IgG1 fc / protein A / fc complex / b-domain
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / 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 / Immunoglobulins / Immunoglobulin-like fold ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsIdusogie, E.E. / Presta, L.G. / Santoro-Gazzano, H. / Totpal, K. / Wong, P.Y. / Ultsch, M. / Meng, Y.G. / Mullkerrin, M.G.
Citation
Journal: J.Immunol. / Year: 2000
Title: Mapping of the C1q binding site on rituxan, a chimeric antibody with a human IgG1 Fc.
Authors: Idusogie, E.E. / Presta, L.G. / Gazzano-Santoro, H. / Totpal, K. / Wong, P.Y. / Ultsch, M. / Meng, Y.G. / Mulkerrin, M.G.
#1: Journal: J.IMMUNOL. / Year: 2001
Title: Engineered Antibodies with Increased Activity to Recruit Complement
Authors: Idusogie, E.E. / Wong, P.Y. / Presta, L.G. / Santoro-Gazzano, H. / Totpal, K. / Ultsch, M. / Mullkerrin, M.G.
#2: Journal: MOL.CELL / Year: 2001
Title: Crystal Structure at 2.8A of an FcRn/Heterodimeric Fc Complex: Mechanism of pH-Dependent Binding
Authors: Martin, W.L. / West Jr., A.P. / Gan, L. / Bjorkman, P.J.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Structural mimicry of a native protein by a minimized binding domain
Authors: Starovasnik, M.A. / Braisted, A.C. / Wells, J.A.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN GAMMA-1 HEAVY CHAIN CONSTANT REGION
B: Minimized B-domain of Protein A Z34C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5263
Polymers27,7382
Non-polymers1,7881
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint31 kcal/mol
Surface area13460 Å2
MethodPISA
2
A: IMMUNOGLOBULIN GAMMA-1 HEAVY CHAIN CONSTANT REGION
B: Minimized B-domain of Protein A Z34C
hetero molecules

A: IMMUNOGLOBULIN GAMMA-1 HEAVY CHAIN CONSTANT REGION
B: Minimized B-domain of Protein A Z34C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0526
Polymers55,4774
Non-polymers3,5752
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11260 Å2
ΔGint50 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.023, 124.774, 90.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody IMMUNOGLOBULIN GAMMA-1 HEAVY CHAIN CONSTANT REGION / Rituximab IgG1 fc fragment


Mass: 23547.598 Da / Num. of mol.: 1 / Fragment: Fc Fragment, Residues 119-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: GenBank: 184747, UniProt: P01857*PLUS
#2: Protein/peptide Minimized B-domain of Protein A Z34C


Mass: 4190.682 Da / Num. of mol.: 1 / Fragment: ENGINEERED PEPTIDE, Residues 6-39 / Source method: obtained synthetically
Details: Phage optimized sequence from the B-domain of Protein A Staphylococcus aureus. Peptide prepared using N-fluorenyl-methoxycarbonyl chemistry on Wang resin.
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1787.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-4-3-1-4-5/a4-b1_a6-j1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1_h4-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 550MME 0.1M NaOAc pH 5.5, 0.25M NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 35573 / Num. obs: 35573 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.036 / Net I/σ(I): 17.8
Reflection shellResolution: 1.65→1.68 Å / Num. unique all: 1619 / Rsym value: 0.133 / % possible all: 88.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.95A Fc-Z34C complex collected at Chess. Fc was solved by molecular replacement using 2.8A 1FC1 Deisenhofer 1981

1fc1


Resolution: 1.65→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3495 10 %RANDOM
Rwork0.206 ---
all0.242 35217 --
obs0.206 35143 94.8 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-20 Å
Luzzati sigma a0.14 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 121 360 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_mcbond_it3.353
X-RAY DIFFRACTIONx_mcangle_it4.483.5
X-RAY DIFFRACTIONx_scbond_it4.756.5
X-RAY DIFFRACTIONx_scangle_it6.975
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 575 9.8 %
Rwork0.289 5299 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM3MOD.CHOTOPH3MOD.CHO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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