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- PDB-4fqc: Crystal Structure of PGT121 Fab Bound to a complex-type sialylate... -

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Basic information

Entry
Database: PDB / ID: 4fqc
TitleCrystal Structure of PGT121 Fab Bound to a complex-type sialylated N-glycan
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / IG FOLD / ANTI HIV / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsScharf, L. / Bjorkman, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies.
Authors: Mouquet, H. / Scharf, L. / Euler, Z. / Liu, Y. / Eden, C. / Scheid, J.F. / Halper-Stromberg, A. / Gnanapragasam, P.N. / Spencer, D.I. / Seaman, M.S. / Schuitemaker, H. / Feizi, T. / ...Authors: Mouquet, H. / Scharf, L. / Euler, Z. / Liu, Y. / Eden, C. / Scheid, J.F. / Halper-Stromberg, A. / Gnanapragasam, P.N. / Spencer, D.I. / Seaman, M.S. / Schuitemaker, H. / Feizi, T. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Advisory / Data collection
Revision 1.2Dec 12, 2012Group: Database references
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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 19, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0264
Polymers48,9462
Non-polymers2,0802
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint5 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.787, 67.787, 94.115
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 heavy chain / Fragment antigen-binding


Mass: 26343.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 22602.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: homo sapiens (human)
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-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: 1916.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-3-1-4-5-3-1-6/a4-b1_a6-j1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f6-g2_h2-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+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 298 K / pH: 5.5
Details: PEG 10000, Bis Tris HCl, CH3COOHNH4, pH 5.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2012
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.209→38.656 Å / Num. obs: 20621 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.161 / Net I/σ(I): 8.7
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.691 / % possible all: 65.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å38.66 Å
Translation2.5 Å38.66 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.656 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 834 4.96 %
Rwork0.201 --
obs0.2031 16831 95.99 %
all-17535 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 141 146 3558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063497
X-RAY DIFFRACTIONf_angle_d0.9494771
X-RAY DIFFRACTIONf_dihedral_angle_d12.9421269
X-RAY DIFFRACTIONf_chiral_restr0.053559
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.55050.35081450.25642686X-RAY DIFFRACTION99
2.5505-2.74740.3351410.24972704X-RAY DIFFRACTION98
2.7474-3.02370.2811400.23172695X-RAY DIFFRACTION99
3.0237-3.4610.24131390.2092634X-RAY DIFFRACTION96
3.461-4.35960.22281310.17072621X-RAY DIFFRACTION93
4.3596-38.66110.18081380.1762657X-RAY DIFFRACTION91
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)
14.7689-0.862-1.59882.5196-0.54742.4136-0.0435-0.2209-0.11480.05720.0406-0.05120.12550.15420.00730.1922-0.0202-0.01820.1453-0.01150.1066-29.1052-1.1426-28.2499
22.5366-1.18810.76710.9378-0.63370.4640.02270.19120.0572-0.0372-0.0892-0.05050.06530.10010.06460.2266-0.01650.00490.1612-0.02140.1292-14.1242-2.6627-21.3212
31.6961-2.41051.82193.8097-2.08442.33490.0004-0.0734-0.02440.4190.3505-0.1511-0.2185-0.1096-0.09710.22230.02030.04660.2215-0.04690.2031-32.79086.341-0.1661
41.7111-1.18350.91972.3118-0.95462.29860.0899-0.224-0.4125-0.04950.16930.40730.232-0.2281-0.25710.20710.0042-0.00080.20090.04270.2884-38.5691-0.4617-10.3279
51.1178-1.44671.29452.7056-1.17571.9606-0.0859-0.23030.02780.09310.16780.1243-0.0261-0.1083-0.11610.1902-0.03760.03270.21930.03990.2713-36.86797.1838-7.7261
63.2976-0.3824-0.43740.57930.27410.1476-0.0408-0.2774-0.070.1612-0.02270.21470.10450.07320.09740.2782-0.00880.00750.20080.0290.1971-17.8283-4.8439-0.6332
73.16741.2101-0.74623.6048-0.62591.7857-0.013-0.06110.0936-0.1689-0.0719-0.2227-0.1490.04910.04360.16510.03180.00950.18910.01040.153-5.12580.8713-8.4189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 51 )
2X-RAY DIFFRACTION2chain 'H' and (resid 52 through 213 )
3X-RAY DIFFRACTION3chain 'L' and (resid 10 through 30 )
4X-RAY DIFFRACTION4chain 'L' and (resid 31 through 61 )
5X-RAY DIFFRACTION5chain 'L' and (resid 62 through 98 )
6X-RAY DIFFRACTION6chain 'L' and (resid 99 through 119 )
7X-RAY DIFFRACTION7chain 'L' and (resid 120 through 209 )

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