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- PDB-4o5l: Crystal structure of broadly neutralizing antibody F045-092 -

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Basic information

Entry
Database: PDB / ID: 4o5l
TitleCrystal structure of broadly neutralizing antibody F045-092
Components
  • Fab F045-092 heavy chain
  • Fab F045-092 light chain
KeywordsIMMUNE SYSTEM / Fab / Fragment antigen binding / Immunoglobulin fold
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / immunoglobulin complex / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ig-like domain-containing protein / Immunoglobulin lambda constant 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5045 Å
AuthorsLee, P.S. / Wilson, I.A.
CitationJournal: Nat Commun / Year: 2014
Title: Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus.
Authors: Lee, P.S. / Ohshima, N. / Stanfield, R.L. / Yu, W. / Iba, Y. / Okuno, Y. / Kurosawa, Y. / Wilson, I.A.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _struct_ref.db_code ..._entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab F045-092 light chain
H: Fab F045-092 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8953
Polymers49,8002
Non-polymers951
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-33 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.515, 77.278, 81.451
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: Antibody Fab F045-092 light chain / Ig lambda chain C region DOT / Ig lambda chain C region NEWM / Ig lambda-3 chain C regions


Mass: 24108.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DOY3
#2: Antibody Fab F045-092 heavy chain


Mass: 25691.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A8K008
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30% PEG 600, 0.1 M phosphate-citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 67979 / Num. obs: 67979 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 22.7
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.51 / % possible all: 83.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7FAB

7fab


Resolution: 1.5045→43.638 Å / SU ML: 0.15 / σ(F): 2 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 3430 5.05 %
Rwork0.1745 --
obs0.1761 67979 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5045→43.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 5 457 3811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013553
X-RAY DIFFRACTIONf_angle_d1.264872
X-RAY DIFFRACTIONf_dihedral_angle_d13.1941280
X-RAY DIFFRACTIONf_chiral_restr0.089552
X-RAY DIFFRACTIONf_plane_restr0.007628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5045-1.5260.31161140.2861851X-RAY DIFFRACTION68
1.526-1.54880.3021390.26062309X-RAY DIFFRACTION84
1.5488-1.5730.24851340.23772430X-RAY DIFFRACTION89
1.573-1.59870.23221310.22942571X-RAY DIFFRACTION94
1.5987-1.62630.25691570.21872722X-RAY DIFFRACTION99
1.6263-1.65590.26511200.20722760X-RAY DIFFRACTION100
1.6559-1.68770.24381690.20132711X-RAY DIFFRACTION100
1.6877-1.72220.24951570.19532730X-RAY DIFFRACTION100
1.7222-1.75960.25191610.19522750X-RAY DIFFRACTION100
1.7596-1.80060.22631370.19172758X-RAY DIFFRACTION100
1.8006-1.84560.23561490.18882719X-RAY DIFFRACTION98
1.8456-1.89550.21571540.17862739X-RAY DIFFRACTION100
1.8955-1.95130.19041400.18042740X-RAY DIFFRACTION100
1.9513-2.01430.23381520.18382770X-RAY DIFFRACTION100
2.0143-2.08630.24351270.17362792X-RAY DIFFRACTION100
2.0863-2.16980.21391430.17382754X-RAY DIFFRACTION99
2.1698-2.26850.21021610.17212723X-RAY DIFFRACTION98
2.2685-2.38810.22361130.17542814X-RAY DIFFRACTION100
2.3881-2.53770.21161640.18112760X-RAY DIFFRACTION100
2.5377-2.73360.20811410.18432801X-RAY DIFFRACTION100
2.7336-3.00870.1971330.18052795X-RAY DIFFRACTION99
3.0087-3.44390.20451440.17272813X-RAY DIFFRACTION99
3.4439-4.33830.17871550.15262811X-RAY DIFFRACTION98
4.3383-43.65680.16661350.14772926X-RAY DIFFRACTION97
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)
11.92330.51830.67721.40231.41554.21090.0239-0.05350.038-0.0249-0.11740.0309-0.1163-0.16630.0850.10190.00430.0030.11440.01360.1122-15.33792.8073.9277
21.9023-0.11630.2223.1889-0.84064.4311-0.0225-0.04220.13990.2291-0.2109-0.0659-0.40720.07420.19740.1764-0.0158-0.02950.1342-0.00790.1592-20.936841.59862.8973
31.3281-0.42910.67733.1087-0.05112.1611-0.09040.0490.0668-0.058-0.0167-0.064-0.19060.09750.09760.13750.0038-0.01380.15930.00890.0992-16.61954.7764-17.4893
43.45340.4907-0.07141.8370.33512.7759-0.0617-0.32080.1076-0.0657-0.0322-0.2499-0.17090.53080.07070.1365-0.0036-0.00150.26220.00010.1984-12.268239.0896-10.7028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:108
2X-RAY DIFFRACTION2chain L and resid 109:300
3X-RAY DIFFRACTION3chain H and resid 1:113
4X-RAY DIFFRACTION4chain H and resid 114:300

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