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- PDB-6cjx: Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of ... -

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Basic information

Entry
Database: PDB / ID: 6cjx
TitleCrystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal form 2)
ComponentsFc fragment of human IgG1
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / LALA MUTATION
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsVan, V. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
CitationJournal: Structure / Year: 2020
Title: Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fc gamma Receptor Binding.
Authors: Orlandi, C. / Deredge, D. / Ray, K. / Gohain, N. / Tolbert, W. / DeVico, A.L. / Wintrode, P. / Pazgier, M. / Lewis, G.K.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.3May 13, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fc fragment of human IgG1
B: Fc fragment of human IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2254
Polymers48,2992
Non-polymers2,9272
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint48 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.000, 74.834, 145.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fc fragment of human IgG1


Mass: 24149.293 Da / Num. of mol.: 2 / Mutation: L234A, L235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 3,350 0.1 M Bus-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2017 / Details: FLAT SI RH COATED M0
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 19011 / % possible obs: 91.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.071 / Net I/σ(I): 20.5
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.749 / Num. unique obs: 710 / CC1/2: 0.741 / Rpim(I) all: 0.399 / % possible all: 69.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVE

3ave


Resolution: 2.44→40.753 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 36.15
RfactorNum. reflection% reflection
Rfree0.2635 971 5.13 %
Rwork0.216 --
obs0.2184 18920 91.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.44→40.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 198 3 3538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143648
X-RAY DIFFRACTIONf_angle_d1.6564998
X-RAY DIFFRACTIONf_dihedral_angle_d7.4822214
X-RAY DIFFRACTIONf_chiral_restr0.076593
X-RAY DIFFRACTIONf_plane_restr0.01612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4369-2.56530.40411100.36191963X-RAY DIFFRACTION71
2.5653-2.7260.37671340.34592275X-RAY DIFFRACTION83
2.726-2.93640.40831430.3162553X-RAY DIFFRACTION92
2.9364-3.23180.34781380.26422717X-RAY DIFFRACTION97
3.2318-3.69920.26541340.21712722X-RAY DIFFRACTION97
3.6992-4.65950.25751340.18262818X-RAY DIFFRACTION99
4.6595-40.75820.20631780.18062901X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3783-0.43060.76351.3427-0.51642.2533-0.11420.30.0043-0.1410.0653-0.0963-0.29410.0452-0.00030.4453-0.02040.04380.3798-0.10540.5236-9.966114.7313-45.0625
24.4329-0.1862-0.28131.80440.2322.6694-0.14030.9446-0.8673-0.30570.1572-0.05690.2555-0.0305-0.01260.4535-0.0765-0.01510.5073-0.21080.662110.8042-7.4792-46.5172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 237 through 444)
2X-RAY DIFFRACTION2(chain 'B' and resid 237 through 445)

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