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- PDB-4gmt: Crystal structure of heterosubtypic Fab S139/1 -

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Basic information

Entry
Database: PDB / ID: 4gmt
TitleCrystal structure of heterosubtypic Fab S139/1
Components
  • Fab S139/1 heavy chain
  • Fab S139/1 light chain
KeywordsIMMUNE SYSTEM / Fab / fragment antigen binding / Immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLee, P.S. / Ekiert, D.C. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Heterosubtypic antibody recognition of the influenza virus hemagglutinin receptor binding site enhanced by avidity.
Authors: Lee, P.S. / Yoshida, R. / Ekiert, D.C. / Sakai, N. / Suzuki, Y. / Takada, A. / Wilson, I.A.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 13, 2023Group: Data collection / Database references ...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
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
L: Fab S139/1 light chain
H: Fab S139/1 heavy chain
M: Fab S139/1 light chain
I: Fab S139/1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4518
Polymers96,6134
Non-polymers8384
Water79344
1
L: Fab S139/1 light chain
H: Fab S139/1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8274
Polymers48,3062
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-41 kcal/mol
Surface area19610 Å2
MethodPISA
2
M: Fab S139/1 light chain
I: Fab S139/1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6244
Polymers48,3062
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-42 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.840, 106.840, 185.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

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Antibody , 2 types, 4 molecules LMHI

#1: Antibody Fab S139/1 light chain


Mass: 23773.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: S139/1 / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five
#2: Antibody Fab S139/1 heavy chain


Mass: 24533.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: S139/1 / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 46 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate, pH 5.5, 2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.497
ReflectionResolution: 2.05→50 Å / Num. all: 76062 / Num. obs: 76062 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.72 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3OZ9 AND 1MEX

3oz9

1mex


Resolution: 2.05→46.292 Å / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 4006 5.28 %GENERATED BY PHENIX.REFINE
Rwork0.1578 ---
obs0.1595 75878 99.66 %-
all-76062 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.922 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0472 Å2-0 Å2-0 Å2
2--2.0472 Å2-0 Å2
3----4.0944 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 52 44 6690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086821
X-RAY DIFFRACTIONf_angle_d1.199290
X-RAY DIFFRACTIONf_dihedral_angle_d16.3032427
X-RAY DIFFRACTIONf_chiral_restr0.0711047
X-RAY DIFFRACTIONf_plane_restr0.0051171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08570.35582020.2943552X-RAY DIFFRACTION94
2.0857-2.12360.28322010.28363557X-RAY DIFFRACTION94
2.1236-2.16440.33522010.2793566X-RAY DIFFRACTION94
2.1644-2.20860.27872010.27973595X-RAY DIFFRACTION95
2.2086-2.25660.25991920.26513561X-RAY DIFFRACTION95
2.2566-2.30910.29991970.25953563X-RAY DIFFRACTION95
2.3091-2.36680.32071970.26213577X-RAY DIFFRACTION95
2.3668-2.43080.3052060.25883626X-RAY DIFFRACTION95
2.4308-2.50230.29871980.24923572X-RAY DIFFRACTION95
2.5023-2.5830.25981980.23663575X-RAY DIFFRACTION95
2.583-2.67530.29051980.21263627X-RAY DIFFRACTION95
2.6753-2.78240.25411990.20483562X-RAY DIFFRACTION95
2.7824-2.90890.2342010.19023590X-RAY DIFFRACTION95
2.9089-3.06220.20171960.17523624X-RAY DIFFRACTION95
3.0622-3.25390.25452040.16693605X-RAY DIFFRACTION95
3.2539-3.50480.2331970.15113601X-RAY DIFFRACTION95
3.5048-3.8570.17692030.12073606X-RAY DIFFRACTION94
3.857-4.4140.15072010.09753598X-RAY DIFFRACTION94
4.414-5.55680.13452010.08413616X-RAY DIFFRACTION94
5.5568-32.75840.17312060.11693660X-RAY DIFFRACTION92
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)
10.0262-0.02240.00770.0678-0.04680.03710.07380.09990.09980.0328-0.08670.0387-0.00870.17310.00390.1153-0.13240.00270.50330.01340.2794-15.318-11.114437.1404
20.03950.0088-0.01360.0038-0.00240.0047-0.0166-0.01010.0267-0.06020.0657-0.0340.0288-0.049400.27230.0899-0.02610.5442-0.02780.2876-2.2777-17.6422.9191
30.02420.04260.02920.20430.03930.04570.08050.13320.01590.0585-0.0048-0.0050.04470.01060.02780.0561-0.0766-0.01550.5677-0.03690.2438-32.9139-20.109125.1652
40.01720.0004-0.00660.0158-0.02050.0198-0.076-0.0042-0.1087-0.0151-0.0591-0.07370.1207-0.1592-0.00090.18710.00030.01920.4531-0.0790.3718-6.3843-33.19193.9683
50.13960.0575-0.04550.0463-0.02670.02630.0106-0.04290.1291-0.0785-0.0096-0.03250.16490.19140.01960.3170.1888-0.00010.44920.01660.280435.3585-23.447164.0285
60.05260.0018-0.0070.01980.00170.0022-0.0199-0.00430.01550.09430.06370.03480.0611-0.00040.01340.33720.1541-0.03740.18320.0170.281536.5914-38.068930.3077
70.02650.00180.01910.00140.00650.04080.047-0.02760.0499-0.0371-0.03490.01260.0557-0.04810.00120.17320.11480.00780.38290.03070.250118.8124-12.837652.3112
80.0079-0.0043-0.01530.0128-0.00110.022-0.00890.023-0.07010.03210.03560.09120.0893-0.063900.30040.0453-0.0280.26580.01940.465320.9967-42.159330.3475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resid 1:118 or chain H and resid 301:302H1 - 118
2X-RAY DIFFRACTION1chain H and resid 1:118 or chain H and resid 301:302H301 - 302
3X-RAY DIFFRACTION2chain H and resid 119:213H119 - 213
4X-RAY DIFFRACTION3chain L and resid 1:109L1 - 109
5X-RAY DIFFRACTION4chain L and resid 110:213L110 - 213
6X-RAY DIFFRACTION5chain I and resid 1:118 or chain I and resid 301:301I1 - 118
7X-RAY DIFFRACTION5chain I and resid 1:118 or chain I and resid 301:301I301
8X-RAY DIFFRACTION6chain I and resid 119:213I119 - 213
9X-RAY DIFFRACTION7chain M and resid 1:109M1 - 109
10X-RAY DIFFRACTION8chain M and resid 110:213M110 - 213

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