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- PDB-5t3z: 3.5 Angstrom Crystal Structure of a Fully and Natively Glycosylat... -

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Basic information

Entry
Database: PDB / ID: 5t3z
Title3.5 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074
Components
  • (Envelope glycoprotein ...) x 2
  • 10-1074 Heavy Chain
  • 10-1074 Light Chain
  • IOMA Heavy Chain
  • IOMA Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / N-linked Glycosylation / Broadly Neutralizing Antibodies / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGristick, H.B. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.
Authors: Gristick, H.B. / von Boehmer, L. / West, A.P. / Schamber, M. / Gazumyan, A. / Golijanin, J. / Seaman, M.S. / Fatkenheuer, G. / Klein, F. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Derived calculations / Category: pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
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.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.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 2.1Apr 13, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 3.0Jan 15, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / diffrn / entity / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._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] / _cell.volume / _diffrn.pdbx_serial_crystal_experiment / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_entity_nonpoly.entity_id / _pdbx_entry_details.has_ligand_of_interest / _pdbx_modification_feature.auth_seq_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns_shell.number_unique_obs / _software.version / _struct_asym.entity_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _symmetry.space_group_name_Hall
Description: Model orientation/position
Details: Updated CDRH3 using coordinates from a high-resolution Fab structure (7TQG)
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,74325
Polymers167,8226
Non-polymers15,92219
Water00
1
B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules

B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules

B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,22975
Polymers503,46518
Non-polymers47,76557
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area76070 Å2
ΔGint-56 kcal/mol
Surface area204360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.258, 217.258, 154.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules BG

#1: Protein Envelope glycoprotein gp160


Mass: 17146.482 Da / Num. of mol.: 1 / Fragment: UNP residues 509-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein Envelope glycoprotein gp160


Mass: 54064.277 Da / Num. of mol.: 1 / Fragment: UNP residues 30-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody , 4 types, 4 molecules HLDE

#3: Antibody 10-1074 Heavy Chain


Mass: 25661.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody 10-1074 Light Chain


Mass: 23180.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody IOMA Heavy Chain


Mass: 25176.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody IOMA Light Chain


Mass: 22591.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 12 types, 19 molecules

#7: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#10: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-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: 1990.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-4[DGlcpNAcb1-2]DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-1-4-3-1-4-5/a4-b1_a6-k1_b4-c1_c3-d1_c6-h1_d2-e1_d4-f1_f4-g1_h2-i1_i4-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1479.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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][a2112h-1b_1-5]/1-1-2-3-1-4-3-1/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#14: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}}LINUCSPDB-CARE
#15: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#16: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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
DManpa1-2DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#17: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#18: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium citrate tribasic pH 7.0 100 mM imidazole pH 7.0 20% PEG MME 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.13
ReflectionResolution: 3.5→64.631 Å / Num. obs: 34373 / % possible obs: 100 % / Redundancy: 61.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.68 / Rpim(I) all: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 3.5→3.67 Å / Redundancy: 59.7 % / Rmerge(I) obs: 9.29 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4992 / CC1/2: 0.4 / Rpim(I) all: 1.21 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Cootmodel building
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T3X

5t3x


Resolution: 3.5→64.63 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.1182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3061 1755 5.11 %
Rwork0.2645 32611 -
obs0.267 34366 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 189.8 Å2
Refinement stepCycle: LAST / Resolution: 3.5→64.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11199 0 1066 0 12265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003812527
X-RAY DIFFRACTIONf_angle_d0.839417048
X-RAY DIFFRACTIONf_chiral_restr0.05472182
X-RAY DIFFRACTIONf_plane_restr0.00532036
X-RAY DIFFRACTIONf_dihedral_angle_d16.10265319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.35561410.31662486X-RAY DIFFRACTION94.63
3.59-3.70.37621460.31932506X-RAY DIFFRACTION94.49
3.7-3.820.31481430.29952492X-RAY DIFFRACTION94.57
3.82-3.960.41071210.32372540X-RAY DIFFRACTION95.38
3.96-4.110.32241280.28482512X-RAY DIFFRACTION95.15
4.12-4.30.28181350.27032510X-RAY DIFFRACTION94.9
4.3-4.530.27341280.25822532X-RAY DIFFRACTION95.19
4.53-4.810.2611190.25722495X-RAY DIFFRACTION95.45
4.81-5.180.27461360.2412514X-RAY DIFFRACTION94.87
5.18-5.70.33451160.25692529X-RAY DIFFRACTION95.58
5.71-6.530.30271700.28312480X-RAY DIFFRACTION93.58
6.53-8.220.34331230.2632506X-RAY DIFFRACTION95.32
8.23-64.630.28611480.23832510X-RAY DIFFRACTION94.36
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)
14.28790270498-1.09396039965-1.72407946514.52796730062.338317275829.39692379931-0.03628411292841.25147479483-0.216102187796-1.277720177770.3368657185330.9969311331631.11778772268-0.555231670264-0.4644969853261.96796615845-0.289318008229-0.0739939308511.625212113990.05228229502851.05306583073-2.61703042926-18.9649438828-22.3968760495
24.275774011690.209508732558-1.066044731933.454796877090.6360483236122.60165322637-0.6373708588851.091437969720.554037460653-1.243271255180.6411003109940.06506936160250.286875512670.5492667734450.09392624628192.18372071183-0.0926109214498-0.2138408694891.27155381731-0.01773601575590.8835584040615.54710392315-6.88684020008-22.4686049398
32.798007725570.99164809157-0.1134811859294.55967351803-0.7222624955030.7096965780990.346282344335-0.230522176256-0.738341085882-0.129412850364-0.306448152827-0.2258717333740.112839859711.681594303820.05559256766982.366386345020.2234504956850.1866473833652.5042932272-0.3341165767791.1990832148316.6221738159-18.4041470072-31.3837199042
40.158062823181-0.1572456193330.3910764444080.165146225364-0.4271452735441.133410504970.73829575331-0.70162582710.0641538058502-0.0698263426377-0.5269567008890.221831396446-0.908091247197-0.153395535512-0.1766474481892.3760052302-0.5337950941650.5267362617322.62173678488-0.4381367797581.4843933752612.58749407737.0746381575-41.8886238339
51.226346340870.1493190083190.6945713839153.88879919252-2.338097449681.898819613690.06612953075770.341933202236-0.26054298895-0.2906394755130.5745382548190.5460927380980.227294420580.089472072173-0.5823987720611.75493610484-0.226694736523-0.000888295474691.73249482412-0.3515717360391.25921405275-1.47612524843-20.3757172638-10.7092959455
63.54426891725-1.01922844289-1.250812765792.130295302192.489691235955.24165847788-0.229684793351-0.276573332539-0.265346893504-0.02917478356610.3604134491460.2631369806890.3040884973060.0104904091991-0.1228868784010.824122067554-0.135308596217-0.03437494368180.6480980044910.03625393699450.957823906859-2.90509286861-18.079832631732.5341673725
71.738458814750.191481370507-0.1348487359390.5257157307340.156566169352.338148725660.03398077890620.43885165304-0.781045226135-0.617437677590.04332768423930.08450345906870.592850086012-0.103769332352-0.03276856132961.27955585783-0.0653236092123-0.05378693994040.739086103817-0.171263225121.103409098820.413400598689-32.347835877310.9402617403
82.621738403850.7208302186010.465467119215.102003032722.522679124856.042423766160.284229752114-0.98540485157-0.4750358902041.686443126140.03505551838350.5085244058270.937228190202-0.650492169285-0.01551071143962.28696713424-0.4943821447330.4851968642081.540693487660.9493005873622.23772416827-19.9253626639-58.984377149271.1522099929
94.7987881198-0.435090127713-0.005708737756323.25112063990.3948073394633.4978951226-0.444669021303-0.388341349746-0.886134056010.0279785411502-0.27529108820.324337729360.707108042190.2852386371220.6587484012071.74947485856-0.3034313086050.1169959409811.261313872670.6922468010822.10848699844-17.083976972-54.308718178659.1101787985
102.845010050280.4787711023840.2008885226044.225631287472.695218465024.302914510361.3632671926-0.886620635656-0.6503670840850.7033844193310.22355209956-0.5457841176670.199349024224-1.07904310006-1.436479640521.83620621702-0.1832165782810.00417891267681.616278005590.4407362260012.1463343949-14.3265905157-55.186589669768.3908868164
111.966969791140.4768380253030.6701612158811.40457766061-0.5263973034370.5967175755680.269174686031-0.449022843361-0.495397448760.6798210456140.3192308898510.3718976372161.3657371519-1.18035448553-0.4409800913862.02288284954-0.4504970053980.001948982516410.9278672045260.2921820308462.00607207454-22.5218045918-52.808925004358.8456988985
121.857668106020.901063768560.788310180143.285541811410.5379487879190.373394175975-0.569262326045-0.861059738513-1.157362053650.5592866985220.08527127398071.162111113441.39127241012-1.071427360780.499801882333.56388399367-1.312687153961.053389779043.39471616290.05396359510032.56137043553-41.4163050849-59.932876448281.6004095931
135.153743514421.933206031830.6510177013062.6983632920.6173132592380.680769233255-0.926310170409-0.66068483539-0.8015612651180.7373587415160.0339253738880.7571918184560.7734978475860.684085555691.023756690823.5617993136-0.7526373214650.2398135933662.493962508920.2416135041641.85869111306-41.8297557559-69.872199241784.2576332164
145.81724229670.895352091172.421518028881.500739261421.313617661772.33633675331-0.597786761382-0.0375576358410.568132706687-0.176028826495-0.6556041421511.38899425841-0.15235194639-0.198694269511.039620334281.910872368630.09285999638150.2943339253862.036200815270.3391563807632.76697519456-43.123132512-38.936581444353.4480746645
153.37424836354-2.850381125580.9790162506573.597086770270.8155685442926.891436505540.980806524251-0.3459269735430.6807623746270.924027732942-0.2137087911941.320720518630.385335587049-2.03912308474-0.617336160871.31807855207-0.3971968878030.1959519888911.578047185070.570259310912.04635735749-29.7129705434-44.320186701352.6138878915
166.31986054304-1.47787990247-0.4913799707531.588303311211.613171360862.521981657380.5183452035680.04616939007320.430698033480.1803201340830.2579771299811.41814350342-0.203507163474-0.863506989903-0.7271904163191.27662120773-0.293955851545-0.06178462023091.432581325180.4758837759972.68953722043-36.0367934117-46.654213725446.0730442042
171.272542716570.59767853970.7084882478072.18296102244-0.62123995745.785758439571.14979298985-0.50668085633-0.4769502990051.010953352420.2344231029741.148546624540.400044697143-1.02581098462-0.9795953959231.29146504339-0.1191109214110.3686583761470.9729333671740.4812680007332.32162462954-23.4824068493-41.799884780652.4581666836
180.4060265536680.5591051823720.1321171186030.990121115588-0.3979363375151.5035554647-0.0364462042425-3.00428072055-0.6111873319160.834012549363-0.08611559024240.6491882806270.279565075059-0.8980759749960.1823042390612.36985069159-0.04463614726381.06851468264.416621258060.4532146833672.71041831991-48.0548785289-52.820705350580.1900955723
191.90624492722-0.4767385577891.193298870842.97210418008-0.8458740018862.86414300163-0.700525646769-1.58217073538-0.215219133180.5733918146740.9446038266550.4506211359440.081747455698-0.372735828633-0.2715957619774.466923313490.2227332469181.941505217013.022208009140.1731230993173.68893217605-51.2719938458-48.279528750181.4379666911
202.011318487790.345017690140.9632969020962.54636080922-0.6125960607920.704002595832-0.156351365175-1.6419967078-0.302296615620.836842861255-0.2444390730231.251658515720.0361748773499-0.2880349993970.4512012072572.87684744338-0.5195909307351.20873195933.18340815918-0.4012335745462.89334792333-48.113650994-46.737918730181.4344848126
213.529341354750.0718160903646-0.7564746077730.4923851949530.2254488405170.2802697670820.21113183234-1.6073740873-0.2978677045211.534936444370.4487479675720.130631044480.144503728347-0.834229900772-0.468537967944.32159051126-0.6348793632061.274415670263.84186364250.846288991772.34273680368-47.0576447166-51.602246454892.5649844674
221.09832441658-1.256746801151.072937047715.91579903244-4.031473892112.83780237107-0.456983530711-1.21055538642-0.1058607432780.3690029009490.8835722930720.2641177123310.684377721481-0.033770584911-0.4096201042323.75124993569-0.8242418245660.6886081362434.47703299569-0.0324535453313.09916140872-56.7607455254-48.343746313389.8784969473
233.00993561593-1.392900317061.72880014825.41158271895-2.098130199134.46884097754-0.139232689161-0.475776539566-0.1721487063691.189103848910.5400050143340.1661707950020.479549038097-0.375263046396-0.3239967959864.11564850846-0.7178536909120.5132650952554.698485481850.5244791709362.57887628712-59.3520744616-52.449529754787.4952105505
246.008982345820.853717720407-0.4971389716854.37955178833-0.1751887401643.14017177017-0.263558982934-0.706050206356-0.761677034578-0.305892538672-0.0400554002993-0.5001937711950.4882838449220.3739309133210.277192166621.115773882170.2367534962870.1892277933651.02060865727-3.46998502087E-51.0542271340528.4608441738-33.312619561826.2936190973
253.273633376472.523697106071.824253446782.88756421133-0.1603230524463.62025046756-0.799047363948-1.741912002560.253930417224-1.22824023703-0.0106046579462-1.74052337196-0.338436529121-0.4615746655961.149822886632.339125074480.5359210014960.1080419263773.504369207570.1385520021644.08876535559.138850658-41.783139277843.0968023697
262.50542358854-0.1005065532741.717045777260.226083703561-0.9749695189164.873121400350.679915101284-0.335114570904-0.86418914321-0.254395212279-0.455685092085-0.1166848197862.400900195970.319484813689-0.1873391984166.920258194340.179107839443-0.9885389607225.583480313510.822470405132.0885644378370.6690686205-52.150898450349.4945092722
272.386526325810.591759762908-1.006926436474.870696532150.1697071772785.43218748255-0.1808264766860.574007021881-1.41741315966-0.231618028786-0.138617554787-0.6876181787810.582361475371.030659913820.3518878636981.198170905570.4540637066150.4428697530471.32806323178-0.0261517461631.4899592273243.9875955122-35.521173896110.3093557517
280.3648494244840.286205984922-0.3009766691971.28430176023-0.973721998490.994790538111.52827958078-1.23288706545-1.763446951910.0864653082871-1.46995643-0.06721895729471.0473830171.13649429138-0.002375773118482.71809825425-0.320722629513-0.668512767334.005067583450.501792658823.0009121127656.8938220007-54.581331961635.6159996799
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CHAIN 'B' AND (RESID 518 THROUGH 571 )BA518 - 5711 - 33
22CHAIN 'B' AND (RESID 572 THROUGH 610 )BA572 - 61034 - 72
33CHAIN 'B' AND (RESID 611 THROUGH 650 )BA611 - 65073 - 112
44CHAIN 'B' AND (RESID 651 THROUGH 664 )BA651 - 664113 - 126
55CHAIN 'G' AND (RESID 31 THROUGH 98 )GB31 - 981 - 68
66CHAIN 'G' AND (RESID 99 THROUGH 190 )GB99 - 19069 - 148
77CHAIN 'G' AND (RESID 191 THROUGH 505 )GB191 - 505149 - 450
88CHAIN 'H' AND (RESID 1 THROUGH 23 )HE1 - 231 - 23
99CHAIN 'H' AND (RESID 24 THROUGH 63 )HE24 - 6324 - 63
1010CHAIN 'H' AND (RESID 64 THROUGH 90 )HE64 - 9064 - 93
1111CHAIN 'H' AND (RESID 91 THROUGH 124 )HE91 - 12494 - 143
1212CHAIN 'H' AND (RESID 125 THROUGH 184 )HE125 - 184144 - 198
1313CHAIN 'H' AND (RESID 185 THROUGH 216 )HE185 - 216199 - 230
1414CHAIN 'L' AND (RESID 8 THROUGH 22 )LF8 - 221 - 15
1515CHAIN 'L' AND (RESID 23 THROUGH 44 )LF23 - 4416 - 37
1616CHAIN 'L' AND (RESID 45 THROUGH 84 )LF45 - 8438 - 80
1717CHAIN 'L' AND (RESID 85 THROUGH 101 )LF85 - 10181 - 100
1818CHAIN 'L' AND (RESID 102 THROUGH 130 )LF102 - 130101 - 129
1919CHAIN 'L' AND (RESID 131 THROUGH 151 )LF131 - 151130 - 150
2020CHAIN 'L' AND (RESID 152 THROUGH 172 )LF152 - 172151 - 171
2121CHAIN 'L' AND (RESID 173 THROUGH 188 )LF173 - 188172 - 187
2222CHAIN 'L' AND (RESID 189 THROUGH 198 )LF189 - 198188 - 197
2323CHAIN 'L' AND (RESID 199 THROUGH 212 )LF199 - 212198 - 211
2424CHAIN 'D' AND (RESID 1 THROUGH 125 )DG1 - 1251 - 138
2525CHAIN 'D' AND (RESID 126 THROUGH 211 )DG126 - 211139 - 224
2626CHAIN 'D' AND (RESID 212 THROUGH 216 )DG212 - 216225 - 229
2727CHAIN 'E' AND (RESID 2 THROUGH 114 )EH2 - 1141 - 114
2828CHAIN 'E' AND (RESID 115 THROUGH 210 )EH115 - 210115 - 210

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