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- PDB-5fyl: Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1... -

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Basic information

Entry
Database: PDB / ID: 5fyl
TitleCrystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22
Components
  • (35O22 ANTIBODY FAB ...) x 2
  • (BG505 GP120 ENV ...) x 2
  • (PGT122 ANTIBODY FAB ...) x 2
KeywordsVIRAL PROTEIN / HIV / ENVELOPE / GLYCAN / TRIMER
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: 3.1 Å
AuthorsStewart-Jones, G.B.E. / Zhou, T. / Thomas, P.V. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2016
Title: Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G
Authors: Stewart-Jones, G.B.E. / Soto, C. / Lemmin, T. / Chuang, G.Y. / Druz, A. / Kong, R. / Thomas, P.V. / Wagh, K. / Zhou, T. / Behrens, A.J. / Bylund, T. / Choi, C.W. / Davison, J.R. / Georgiev, ...Authors: Stewart-Jones, G.B.E. / Soto, C. / Lemmin, T. / Chuang, G.Y. / Druz, A. / Kong, R. / Thomas, P.V. / Wagh, K. / Zhou, T. / Behrens, A.J. / Bylund, T. / Choi, C.W. / Davison, J.R. / Georgiev, I.S. / Joyce, M.G. / Kwon, Y.D. / Pancera, M. / Taft, J. / Yang, Y. / Zhang, B. / Shivatare, S.S. / Shivatare, V.S. / Lee, C.C.D. / Wu, C.Y. / Bewley, C.A. / Burton, D.R. / Koff, W.C. / Connors, M. / Crispin, M. / Korber, B.T. / Wong, C.H. / Mascola, J.R. / Kwong, P.D.
History
DepositionMar 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references / Other / Refinement description
Revision 1.3May 18, 2016Group: Database references
Revision 1.4Jul 20, 2016Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.5Aug 3, 2016Group: Structure summary
Revision 1.6Jul 12, 2017Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: BG505 GP120 ENV ECTODOMAIN
D: 35O22 ANTIBODY FAB HEAVY CHAIN
E: 35O22 ANTIBODY FAB LIGHT CHAIN
G: BG505 GP120 ENV ECTODOMAIN
H: PGT122 ANTIBODY FAB HEAVY CHAIN
L: PGT122 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,56928
Polymers170,0466
Non-polymers20,52222
Water00
1
B: BG505 GP120 ENV ECTODOMAIN
D: 35O22 ANTIBODY FAB HEAVY CHAIN
E: 35O22 ANTIBODY FAB LIGHT CHAIN
G: BG505 GP120 ENV ECTODOMAIN
H: PGT122 ANTIBODY FAB HEAVY CHAIN
L: PGT122 ANTIBODY FAB LIGHT CHAIN
hetero molecules

B: BG505 GP120 ENV ECTODOMAIN
D: 35O22 ANTIBODY FAB HEAVY CHAIN
E: 35O22 ANTIBODY FAB LIGHT CHAIN
G: BG505 GP120 ENV ECTODOMAIN
H: PGT122 ANTIBODY FAB HEAVY CHAIN
L: PGT122 ANTIBODY FAB LIGHT CHAIN
hetero molecules

B: BG505 GP120 ENV ECTODOMAIN
D: 35O22 ANTIBODY FAB HEAVY CHAIN
E: 35O22 ANTIBODY FAB LIGHT CHAIN
G: BG505 GP120 ENV ECTODOMAIN
H: PGT122 ANTIBODY FAB HEAVY CHAIN
L: PGT122 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,70684
Polymers510,13918
Non-polymers61,56766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area130110 Å2
ΔGint239.5 kcal/mol
Surface area248470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.780, 129.780, 313.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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BG505 GP120 ENV ... , 2 types, 2 molecules BG

#1: Protein BG505 GP120 ENV ECTODOMAIN


Mass: 17146.482 Da / Num. of mol.: 1 / Fragment: GP120 ENV ECTODOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Cell: T-CELL / Gene: ENV / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: Q2N0S6
#4: Protein BG505 GP120 ENV ECTODOMAIN


Mass: 54064.277 Da / Num. of mol.: 1 / Fragment: GP120 ENV ECTODOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Cell: T-CELL / Gene: ENV / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: Q2N0S6

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Antibody , 4 types, 4 molecules DEHL

#2: Antibody 35O22 ANTIBODY FAB HEAVY CHAIN


Mass: 26170.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T / Production host: HOMO SAPIENS (human)
#3: Antibody 35O22 ANTIBODY FAB LIGHT CHAIN


Mass: 23318.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T / Production host: HOMO SAPIENS (human)
#5: Antibody PGT122 ANTIBODY FAB HEAVY CHAIN


Mass: 26465.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)
#6: Antibody PGT122 ANTIBODY FAB LIGHT CHAIN


Mass: 22880.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)

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Sugars , 15 types, 22 molecules

#7: 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
#8: 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.: 2
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
#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[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/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_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)][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
#11: 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-(1-3)-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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-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)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]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]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#13: 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
#14: 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-(1-2)-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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#15: 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
#16: 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)]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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#17: 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-(1-3)-[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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]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-j1_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)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#18: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[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]/1-1-2-3-3-3/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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#19: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#20: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#21: 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.: 4
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.52 % / Description: NONE
Crystal growpH: 5.5
Details: 0.18 M LI2SO4, 4.79% PEG 1500, 14.4% ISOPROPANOL, 10 MM YTTRIUM CHLORIDE, 0.09 M SODIUM ACETATE PH 5.5

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 53617 / % possible obs: 85.1 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 4.82

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4TVP

4tvp


Resolution: 3.1→40.998 Å / σ(F): 1.36 / Phase error: 33.29 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3072 1710 5.4 %
Rwork0.2503 --
obs0.2537 31517 58.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→40.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 1374 0 12718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513142
X-RAY DIFFRACTIONf_angle_d0.96118065
X-RAY DIFFRACTIONf_dihedral_angle_d14.975069
X-RAY DIFFRACTIONf_chiral_restr0.0362366
X-RAY DIFFRACTIONf_plane_restr0.0042081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.20030.3631310.3202566X-RAY DIFFRACTION12
3.2003-3.31450.3897380.3151773X-RAY DIFFRACTION16
3.3145-3.44710.3733610.31671071X-RAY DIFFRACTION22
3.4471-3.60380.36760.29961425X-RAY DIFFRACTION29
3.6038-3.79360.35381070.29631967X-RAY DIFFRACTION41
3.7936-4.03090.33131520.27332775X-RAY DIFFRACTION57
4.0309-4.34140.31971860.24853381X-RAY DIFFRACTION69
4.3414-4.77720.26762030.22644000X-RAY DIFFRACTION82
4.7772-5.46570.27632410.22954627X-RAY DIFFRACTION94
5.4657-6.87590.33412460.26084649X-RAY DIFFRACTION95
6.8759-32.94470.29172530.23884673X-RAY DIFFRACTION95
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)
11.61730.0255-0.92242.0006-1.10821.8659-0.0427-0.48880.2570.474-0.08840.3823-0.4427-0.3133-0.1057-0.08660.6771-0.3927-0.37220.31541.135651.765134.42919.7997
22.95022.14120.86242.88740.8720.4473-0.2175-0.4594-0.36390.1636-0.06680.27140.17820.1778-0.12620.9050.28050.24851.0492-0.11470.596748.208544.197430.6465
32.0695-0.67890.17421.63330.13860.60180.0989-0.1896-0.23060.3078-0.01930.8496-0.2869-0.2322-0.07311.2858-0.34970.2841.884-0.31971.33818.986224.233830.4309
40.42490.19150.46190.38120.20680.49580.08090.01820.28870.137-0.16960.1986-0.2689-0.07810.04392.60180.05120.06552.2269-0.05372.3883-11.565342.278526.8062
51.7508-0.25920.7351.17570.58130.71530.1093-0.25280.24440.65740.05740.28510.0442-0.0674-0.11161.65840.11920.48661.9241-0.13091.365119.193832.545148.9448
60.0741-0.11350.02310.1597-0.0360.01180.2179-0.11120.08330.2348-0.1356-0.06030.1173-0.2882-0.10042.59380.19950.40942.26430.15362.2198-12.333843.230741.8049
70.7636-1.0620.20521.5257-0.11410.71670.2155-0.26290.14650.2396-0.1250.43980.2290.0241-0.0862.53410.1450.28582.39360.09062.7171-19.670441.623844.7501
82.97420.00320.20772.527-1.58190.9765-0.04140.7964-0.2822-0.596-0.5273-0.04040.09610.03470.39270.29950.0680.39740.6042-0.13331.317452.289226.97766.3487
91.2089-0.0087-0.66260.8728-0.05611.6092-0.59090.6902-0.0606-2.67150.28250.80090.5813-0.99020.1047-2.36080.77730.2780.5555-0.34940.785447.011224.3692-20.5343
100.5494-0.07220.28570.1930.10970.8185-0.14870.06830.095-0.5980.82151.0612-0.5211-2.02790.0136-1.0217-0.31710.18340.2198-0.43361.387435.089620.0681-16.0738
110.0492-0.39580.45742.9573-3.25573.5634-0.0242-0.1877-0.3535-0.43830.08720.4506-0.1387-0.3353-0.08161.82720.14530.28232.0342-0.26651.477723.7567-12.8711-69.3562
121.9247-2.53071.4175.5292-3.02961.682-0.1176-0.18320.10680.59940.39260.4021-0.5199-0.491-0.1951.6040.1760.15231.5414-0.68431.00429.0228-3.8692-64.2703
130.0757-0.2561-0.29291.29770.79131.2115-0.04290.2555-0.4747-0.9549-0.07260.5017-0.016-0.51150.4940.9668-0.10350.26991.54-0.69481.229729.5117-6.2247-57.3926
140.3646-0.34930.1881.29370.41430.40110.2712-0.2103-0.1264-0.1284-0.1676-0.1878-0.30660.2651-0.20861.44930.23190.33621.2382-0.1541.449936.6077-26.4675-86.5966
156.3908-0.05431.31186.8709-4.38343.05590.7457-0.3495-0.36770.70960.23980.31740.1240.186-1.05811.82440.19460.45681.52290.18841.322733.4225-25.4371-84.4968
162.7577-0.8003-0.47533.66281.62480.74140.18920.0119-0.31040.3115-0.28880.98740.1371-0.2919-0.09980.9822-0.0078-0.00541.4587-0.25931.366634.7419-32.2781-85.7737
171.2276-0.33110.56111.12710.14910.62850.1921-0.0359-0.6134-0.4541-0.0157-0.04280.5255-0.34020.1860.7548-0.34760.06611.1159-0.62561.302445.2715-13.8214-53.424
181.00591.39990.63953.51530.60340.55160.22310.11960.0577-0.2188-0.0340.1491-0.2122-0.4243-0.1690.59890.15290.19251.4936-0.27011.190251.9568-30.4453-87.3515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 518 THROUGH 616 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 617 THROUGH 664 )
3X-RAY DIFFRACTION3CHAIN 'D' AND (RESID 1 THROUGH 147 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 148 THROUGH 224 )
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 2 THROUGH 102 )
6X-RAY DIFFRACTION6CHAIN 'E' AND (RESID 103 THROUGH 148 )
7X-RAY DIFFRACTION7CHAIN 'E' AND (RESID 149 THROUGH 210 )
8X-RAY DIFFRACTION8CHAIN 'G' AND (RESID 31 THROUGH 77 )
9X-RAY DIFFRACTION9CHAIN 'G' AND (RESID 78 THROUGH 255 )
10X-RAY DIFFRACTION10CHAIN 'G' AND (RESID 256 THROUGH 505 )
11X-RAY DIFFRACTION11CHAIN 'H' AND (RESID 1 THROUGH 32 )
12X-RAY DIFFRACTION12CHAIN 'H' AND (RESID 33 THROUGH 72 )
13X-RAY DIFFRACTION13CHAIN 'H' AND (RESID 73 THROUGH 101 )
14X-RAY DIFFRACTION14CHAIN 'H' AND (RESID 102 THROUGH 140 )
15X-RAY DIFFRACTION15CHAIN 'H' AND (RESID 141 THROUGH 155 )
16X-RAY DIFFRACTION16CHAIN 'H' AND (RESID 156 THROUGH 211 )
17X-RAY DIFFRACTION17CHAIN 'L' AND (RESID 6 THROUGH 101 )
18X-RAY DIFFRACTION18CHAIN 'L' AND (RESID 102 THROUGH 210 )

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