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

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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 ChainInstitute of Mathematics and Applications, Bhubaneswar
  • IOMA Light ChainInstitute of Mathematics and Applications, Bhubaneswar
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 / 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 / identical protein binding / plasma 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)184,25525
Polymers167,8226
Non-polymers16,43319
Water0
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)552,76475
Polymers503,46518
Non-polymers49,29957
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)217.258, 217.258, 154.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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 / Institute of Mathematics and Applications, Bhubaneswar


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 / Institute of Mathematics and Applications, Bhubaneswar


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 , 13 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-Glycam 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
[]{[(4+1)][b-D-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-Glycam 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
[]{[(4+1)][b-D-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-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
#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-Glycam 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
[]{[(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-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(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]{}}}}}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-Glycam 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
[]{[(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+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-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-f1_d2-e1_f3-g1WURCSPDB2Glycan 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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#14: 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)-[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: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-4-3-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1WURCSPDB2Glycan 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+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#15: 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-Glycam 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
[]{[(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]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#16: 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-Glycam 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
[]{[(4+1)][b-D-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
#17: 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-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_f2-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]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#18: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#19: 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.: 2
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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Experimental details

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Experiment

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

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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
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 / CC1/2: 0.4 / Rpim(I) all: 1.21 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T3X

5t3x


Resolution: 3.5→64.631 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 39.15 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2984 1755 5.11 %
Rwork0.2751 --
obs0.2781 34366 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→64.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11200 0 1101 0 12301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412671
X-RAY DIFFRACTIONf_angle_d1.117403
X-RAY DIFFRACTIONf_dihedral_angle_d13.6857443
X-RAY DIFFRACTIONf_chiral_restr0.0541915
X-RAY DIFFRACTIONf_plane_restr0.0042057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5008-3.59540.36561410.33872486X-RAY DIFFRACTION95
3.5954-3.70120.37221460.3342524X-RAY DIFFRACTION95
3.7012-3.82060.33961450.31542488X-RAY DIFFRACTION94
3.8206-3.95710.44061190.34642542X-RAY DIFFRACTION95
3.9571-4.11550.3411300.30792494X-RAY DIFFRACTION95
4.1155-4.30270.27491330.28932512X-RAY DIFFRACTION95
4.3027-4.52940.28081300.27782528X-RAY DIFFRACTION95
4.5294-4.8130.28131170.27022501X-RAY DIFFRACTION96
4.813-5.18440.26161360.25452502X-RAY DIFFRACTION95
5.1844-5.70550.36241160.272529X-RAY DIFFRACTION96
5.7055-6.52980.30871700.29872480X-RAY DIFFRACTION94
6.5298-8.22170.32361230.27382506X-RAY DIFFRACTION95
8.2217-52.39360.27331480.22962505X-RAY DIFFRACTION94
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)
10.3065-0.01490.00730.03390.03140.00390.04690.49150.4756-0.80910.95460.36060.4080.05790.0252.3716-0.2736-0.05372.0391-0.01271.0101-2.5824-18.9486-22.431
20.14220.1798-0.05470.23720.0850.1611-0.27160.31950.4537-0.60740.68020.2356-0.05550.52430.00152.32550.0176-0.14911.5385-0.05190.98235.5283-6.8296-22.4757
30.1712-0.15010.07030.1358-0.03190.05650.0051-0.2423-0.38090.1138-0.18570.82020.050.6548-0.00022.57120.13680.34152.6224-0.34141.205416.6144-18.4016-31.4136
40.0474-0.0447-0.03510.0250.02650.03250.5182-0.5197-0.3052-0.3063-0.3220.2304-0.1771-0.04350.00062.5876-0.52710.50872.5607-0.19211.501312.59277.0919-41.9202
50.2144-0.1348-0.04150.9781-0.7060.41530.04970.1548-0.2378-0.0270.41250.317-0.07160.16440.00021.8351-0.11050.06621.7809-0.34081.2919-1.4688-20.349-10.7089
60.745-0.1283-0.06330.05030.2610.5409-0.1363-0.1525-0.1121-0.19090.18320.1368-0.14350.25410.00010.9479-0.04740.00610.69660.03110.8304-2.914-18.051932.5399
70.96760.0751-0.0975-0.07060.03920.65250.00730.0606-0.5669-0.31280.05040.22660.0726-0.1883-0.00431.031-0.0959-0.0350.5381-0.15620.82440.4171-32.344110.9401
80.1167-0.079-0.02830.09580.01460.0041-0.3768-0.3006-0.09660.41260.03820.4679-0.25390.0937-0.00132.4526-0.54410.38491.8330.80892.059-19.9097-59.006171.1169
90.4341-0.12790.41790.1953-0.20240.4797-0.1951-0.118-0.1244-0.2297-0.58810.5211-0.01170.3274-0.00011.7767-0.26790.21821.33310.66372.0805-17.1165-54.283659.1337
100.133-0.09740.03520.1829-0.12140.08150.8645-0.506-0.56780.03850.055-0.197-0.3377-0.74250.00052.0515-0.24880.07621.66470.34182.1282-14.3107-55.165268.3268
110.8154-0.30070.24830.2416-0.1350.05280.59380.0933-0.4890.21920.1093-0.08070.6669-0.49660.98471.5225-0.5779-0.18850.49190.35021.5258-22.5138-52.813558.8759
120.1299-0.0585-0.11240.13290.04510.0559-0.5871-0.3032-0.64580.25620.3610.42750.4755-0.10950.00013.2904-1.27280.82483.0398-0.02742.4369-41.4067-59.897781.5801
130.5614-0.4741-0.29191.21010.67020.3713-1.1340.1083-0.37850.2904-0.13010.45980.50750.7501-0.1483.7831-0.98430.122.56640.38821.9367-41.8035-69.812184.2942
140.0303-0.03240.01420.0396-0.02920.0135-0.4348-0.03390.2228-0.1235-0.28980.61350.01420.14520.00052.10170.10530.03882.18990.33152.9219-43.1201-38.941753.5132
150.156-0.15260.01310.18720.060.10310.62070.13420.07950.0367-0.57130.16030.6609-0.4339-0.00021.2378-0.30350.02611.27050.45191.8142-29.7119-44.311652.613
161.2412-0.21890.44050.5483-0.07160.1680.45940.2754-0.352-0.3293-0.19610.52340.25590.07880.10141.0898-0.2988-0.07011.19290.42022.3669-36.0443-46.656146.1509
170.35240.03140.350.00250.01670.34670.68180.1775-0.41490.2929-0.02130.23580.2777-0.00220.0841.2967-0.09770.32690.840.37822.0095-23.4732-41.807252.4897
180.08360.16380.35951.07690.35871.4481-0.0679-1.21790.3477-0.0965-0.40650.3553-0.0414-0.6761-0.19361.8069-0.1611.16213.30420.27972.4853-48.0562-52.824880.1945
190.0459-0.0501-0.0490.03390.03470.0413-0.2684-0.4912-0.20730.04480.3778-0.06320.12640.0004-0.00024.24950.03311.64363.54620.50673.6531-51.2774-48.293781.456
200.03030.00330.01090.0209-0.02260.0237-0.0451-0.2855-0.5767-0.279-0.27880.5907-0.00170.05420.00033.1143-0.2990.96853.2674-0.42752.8256-48.1097-46.774881.4277
210.15210.08680.05830.050.06270.1137-0.0433-0.1630.13290.26060.1629-0.1541-0.0284-0.18930.023.4721-0.34521.18563.40510.66031.5009-47.1227-51.608992.5771
220.02590.0041-0.0019-0.0001-0.01810.0264-0.1044-0.44610.1004-0.10540.3393-0.0872-0.04580.0429-0.00054.1793-0.38660.624.26720.01533.1355-56.7299-48.332689.9332
230.04280.00030.03310.0084-0.00270.0188-0.15720.310.23670.1860.1248-0.05330.190.07080.00033.95-0.5110.33514.26510.86882.7609-59.2928-52.44587.5338
241.02770.5005-0.54040.5295-0.58390.6142-0.1937-0.4689-0.0374-0.5283-0.1975-0.23510.08950.1183-0.07821.13910.23560.1641.05470.03771.008128.3559-33.088426.3307
250.0594-0.0170.0651-0.0142-0.00180.0397-0.9074-0.4532-0.0274-0.9109-0.5045-0.89220.0456-1.016-0.00022.82610.41930.02474.36880.1424.407359.1442-41.758543.1263
260.06990.07010.05850.33220.32360.31730.1278-0.0813-0.09950.02130.01560.00320.09510.07330.01656.6750.2959-0.42944.75170.8231.682970.7735-52.364849.5165
270.4496-0.3021-0.32121.1389-0.94152.0295-0.27010.2982-0.5747-0.0309-0.6335-0.35710.34140.928-0.98470.91790.67780.81010.8814-0.02141.076643.9781-35.562510.3109
280.1363-0.00760.08210.18280.17970.15011.2601-0.2337-0.5166-0.0837-1.04770.06220.01780.3805-0.00022.3605-0.2233-0.45053.62740.2722.70156.9343-54.560435.6313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 518 through 571 )
2X-RAY DIFFRACTION2chain 'B' and (resid 572 through 610 )
3X-RAY DIFFRACTION3chain 'B' and (resid 611 through 650 )
4X-RAY DIFFRACTION4chain 'B' and (resid 651 through 664 )
5X-RAY DIFFRACTION5chain 'G' and (resid 31 through 98 )
6X-RAY DIFFRACTION6chain 'G' and (resid 99 through 190 )
7X-RAY DIFFRACTION7chain 'G' and (resid 191 through 505 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 23 )
9X-RAY DIFFRACTION9chain 'H' and (resid 24 through 63 )
10X-RAY DIFFRACTION10chain 'H' and (resid 64 through 90 )
11X-RAY DIFFRACTION11chain 'H' and (resid 91 through 124 )
12X-RAY DIFFRACTION12chain 'H' and (resid 125 through 184 )
13X-RAY DIFFRACTION13chain 'H' and (resid 185 through 216 )
14X-RAY DIFFRACTION14chain 'L' and (resid 8 through 22 )
15X-RAY DIFFRACTION15chain 'L' and (resid 23 through 44 )
16X-RAY DIFFRACTION16chain 'L' and (resid 45 through 84 )
17X-RAY DIFFRACTION17chain 'L' and (resid 85 through 101 )
18X-RAY DIFFRACTION18chain 'L' and (resid 102 through 130 )
19X-RAY DIFFRACTION19chain 'L' and (resid 131 through 151 )
20X-RAY DIFFRACTION20chain 'L' and (resid 152 through 172 )
21X-RAY DIFFRACTION21chain 'L' and (resid 173 through 188 )
22X-RAY DIFFRACTION22chain 'L' and (resid 189 through 198 )
23X-RAY DIFFRACTION23chain 'L' and (resid 199 through 212 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 125 )
25X-RAY DIFFRACTION25chain 'D' and (resid 126 through 211 )
26X-RAY DIFFRACTION26chain 'D' and (resid 212 through 216 )
27X-RAY DIFFRACTION27chain 'E' and (resid 2 through 114 )
28X-RAY DIFFRACTION28chain 'E' and (resid 115 through 210 )

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