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- PDB-4dqo: Crystal Structure of PG16 Fab in Complex with V1V2 Region from HI... -

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Entry
Database: PDB / ID: 4dqo
TitleCrystal Structure of PG16 Fab in Complex with V1V2 Region from HIV-1 strain ZM109
Components
  • 1FD6-V1V2 scaffold ZM109 HIV-1 strain
  • PG16 Fab Heavy Chain
  • PG16 Fab Light Chain
KeywordsIMMUNE SYSTEM / immunoglobulin / immune recognition / glycan / HIV-1 / V1V2 / Envelope glycoprotein
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Immunoglobulins / Roll ...Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.438 Å
AuthorsPancera, M. / McLellan, J.S. / Kwong, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for diverse N-glycan recognition by HIV-1-neutralizing V1-V2-directed antibody PG16.
Authors: Pancera, M. / Shahzad-Ul-Hussan, S. / Doria-Rose, N.A. / McLellan, J.S. / Bailer, R.T. / Dai, K. / Loesgen, S. / Louder, M.K. / Staupe, R.P. / Yang, Y. / Zhang, B. / Parks, R. / Eudailey, J. ...Authors: Pancera, M. / Shahzad-Ul-Hussan, S. / Doria-Rose, N.A. / McLellan, J.S. / Bailer, R.T. / Dai, K. / Loesgen, S. / Louder, M.K. / Staupe, R.P. / Yang, Y. / Zhang, B. / Parks, R. / Eudailey, J. / Lloyd, K.E. / Blinn, J. / Alam, S.M. / Haynes, B.F. / Amin, M.N. / Wang, L.X. / Burton, D.R. / Koff, W.C. / Nabel, G.J. / Mascola, J.R. / Bewley, C.A. / Kwong, P.D.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Derived calculations / Other
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jul 24, 2013Group: Database references
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 3.1May 19, 2021Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PG16 Fab Heavy Chain
L: PG16 Fab Light Chain
C: 1FD6-V1V2 scaffold ZM109 HIV-1 strain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1615
Polymers63,0343
Non-polymers3,1272
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint39 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.054, 207.561, 87.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody PG16 Fab Heavy Chain


Mass: 26831.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F GnTI- / Production host: Homo sapiens (human)
#2: Antibody PG16 Fab Light Chain


Mass: 22713.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVRC8400 / Cell line (production host): HEK293F GnTI- / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 149 molecules C

#3: Protein 1FD6-V1V2 scaffold ZM109 HIV-1 strain


Mass: 13489.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: PVRC8400 / Cell line (production host): HEK293F GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q6TCP8*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1891.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-1-4-5-3-3-3/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f6-g2_h3-i1_h6-j1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Isopropanol, 15% PEG 3550, 0.2M ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. all: 25408 / Num. obs: 25408 / % possible obs: 91 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.174 / Rsym value: 0.181 / Net I/σ(I): 8.7
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1700 / % possible all: 61.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MUG

3mug


Resolution: 2.438→45.112 Å / SU ML: 0.79 / σ(F): 1.35 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 1271 5.02 %Random
Rwork0.2014 ---
obs0.2028 25294 90.33 %-
all-25294 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.99 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.8664 Å2-0 Å2-0 Å2
2---7.0669 Å2-0 Å2
3----5.7995 Å2
Refinement stepCycle: LAST / Resolution: 2.438→45.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 211 148 4468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024457
X-RAY DIFFRACTIONf_angle_d0.7236079
X-RAY DIFFRACTIONf_dihedral_angle_d24.3341656
X-RAY DIFFRACTIONf_chiral_restr0.042731
X-RAY DIFFRACTIONf_plane_restr0.003737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4383-2.53590.3251960.30681778X-RAY DIFFRACTION61
2.5359-2.65130.31581170.27872123X-RAY DIFFRACTION73
2.6513-2.7910.2781320.26482469X-RAY DIFFRACTION85
2.791-2.96590.28151570.23882796X-RAY DIFFRACTION96
2.9659-3.19480.27871370.23162920X-RAY DIFFRACTION99
3.1948-3.51620.27051580.21862914X-RAY DIFFRACTION99
3.5162-4.02470.2151660.18762942X-RAY DIFFRACTION100
4.0247-5.06960.16961590.14642992X-RAY DIFFRACTION100
5.0696-45.11950.19831490.18583089X-RAY DIFFRACTION99
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)
12.1530.83540.72863.99492.40224.6894-0.039-0.0789-0.0206-0.05510.1204-0.06750.2249-0.0201-0.09110.2391-0.01780.00590.22110.0460.115423.9581-61.969417.6696
22.2388-0.2472-0.16164.6076-1.434.4944-0.06350.31460.4274-0.11380.20170.5816-0.5804-0.4884-0.08730.29090.01080.0090.3710.07980.345118.7476-30.625911.386
31.7023-0.19190.41924.6523-1.67943.60930.04760.1126-0.2231-0.0246-0.0028-0.21260.50530.254-0.00220.31590.0531-0.03410.2781-0.04420.162627.411-67.3476-1.7159
42.90630.32940.49114.57561.20576.6350.02580.25840.5511-0.00870.3111-0.0159-0.2638-0.1865-0.26640.4619-0.1082-0.00280.31960.13810.346531.4571-26.39233.0097
50.63980.7527-0.78212.797-0.37211.1041-0.071-0.3434-0.72420.40210.04720.2110.62520.1205-0.08371.0421-0.00360.05840.42620.0360.817919.9505-99.49118.2109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:110
2X-RAY DIFFRACTION2chain L and resid 111:210
3X-RAY DIFFRACTION3chain H and resid 1:137
4X-RAY DIFFRACTION4chain H and resid 138:216
5X-RAY DIFFRACTION5chain C and resid 119:317

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