[English] 日本語
Yorodumi
- PDB-5es4: RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5es4
TitleRE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION
Components
  • Integrin alpha-X
  • Integrin beta-2
KeywordsCELL ADHESION / Complement Receptor-4 alphaXbeta2
Function / homology
Function and homology information


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / cellular extravasation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / cellular extravasation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / negative regulation of dopamine metabolic process / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / phagocytosis, engulfment / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / specific granule membrane / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / secretory granule membrane / positive regulation of superoxide anion generation / cell-matrix adhesion / animal organ morphogenesis / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor tyrosine kinase binding / receptor internalization / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / integrin binding / cell-cell signaling / extracellular vesicle / regulation of cell shape / signaling receptor activity / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / defense response to virus / receptor complex / cell adhesion / positive regulation of cell migration / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / protein kinase binding / cell surface / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt ...ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-2 / Integrin alpha-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsSen, M. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI CA031798 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.
Authors: Sen, M. / Springer, T.A.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-X
B: Integrin beta-2
C: Integrin alpha-X
D: Integrin beta-2
E: Integrin alpha-X
F: Integrin beta-2
G: Integrin alpha-X
H: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)847,07169
Polymers824,9498
Non-polymers22,12261
Water1,20767
1
A: Integrin alpha-X
B: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,14118
Polymers206,2372
Non-polymers5,90416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-X
D: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,53016
Polymers206,2372
Non-polymers5,29314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Integrin alpha-X
F: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,42717
Polymers206,2372
Non-polymers5,19015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Integrin alpha-X
H: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,97318
Polymers206,2372
Non-polymers5,73516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.030, 163.480, 536.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Integrin alpha-X / CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain ...CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95


Mass: 125606.438 Da / Num. of mol.: 4 / Fragment: UNP residues 20-1103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAX, CD11C / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P20702
#2: Protein
Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 80630.695 Da / Num. of mol.: 4 / Fragment: UNP residues 23-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05107

-
Sugars , 13 types, 44 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d6-e1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-6)-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
DManpa1-6DManpa1-2DManpa1-3[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_e6-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]{[(6+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
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 1
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
#7: 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
#8: 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.: 2
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
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-6[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_e6-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]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#10: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}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-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 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[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_e6-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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: 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-(1-6)]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[DManpa1-6DManpa1-6]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_f6-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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#14: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_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]{}}}}}}LINUCSPDB-CARE
#17: 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.: 27
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

-
Non-polymers , 3 types, 84 molecules

#15: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, TEMPERATURE 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 198644 / % possible obs: 98.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 9.46
Reflection shellHighest resolution: 3.15 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.3→49.51 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1819 1.04 %Random selection
Rwork0.257 ---
obs0.258 174325 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49499 0 1432 67 50998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752369
X-RAY DIFFRACTIONf_angle_d1.18371193
X-RAY DIFFRACTIONf_dihedral_angle_d10.66231783
X-RAY DIFFRACTIONf_chiral_restr0.0688134
X-RAY DIFFRACTIONf_plane_restr0.0069200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38920.43751370.449712994X-RAY DIFFRACTION98
3.3892-3.48890.43331390.403813054X-RAY DIFFRACTION99
3.4889-3.60150.43231440.374813110X-RAY DIFFRACTION100
3.6015-3.73020.39781290.341213152X-RAY DIFFRACTION100
3.7302-3.87950.3711330.315413187X-RAY DIFFRACTION99
3.8795-4.0560.3471350.292913120X-RAY DIFFRACTION99
4.056-4.26970.30891400.274413243X-RAY DIFFRACTION100
4.2697-4.5370.28521560.236613235X-RAY DIFFRACTION100
4.537-4.8870.27641480.215213264X-RAY DIFFRACTION100
4.887-5.37830.29831390.224213305X-RAY DIFFRACTION100
5.3783-6.15530.31221260.247413411X-RAY DIFFRACTION100
6.1553-7.75020.31191570.272113539X-RAY DIFFRACTION100
7.7502-49.51230.25481360.214413892X-RAY DIFFRACTION100
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)
10.535-0.02810.424-0.0194-0.01361.97360.0710.28770.15360.53120.082-0.11480.2526-0.2792-0.00071.09070.1686-0.18970.88940.05831.0174-23.847519.0553-13.0643
20.0742-0.29790.43790.6161-0.36621.38610.2080.1018-0.0881-0.567-0.3229-0.00150.69080.663201.1710.0772-0.05840.99720.0620.9151-21.838713.132233.4337
31.80.9671-1.45030.7717-0.85561.0714-0.24470.2449-0.0668-0.22380.1569-0.07960.1134-0.114500.8846-0.085-0.00630.61250.0210.9151-2.902424.348149.6324
41.20290.4320.09392.42270.3704-0.20990.50140.27-0.3386-1.2947-0.2348-0.3760.70220.7436-0.03343.06120.97270.32940.7163-0.21491.4059-10.1912-17.461219.782
50.87521.2471.03250.04730.22680.7341-0.3774-0.0308-0.1027-1.25140.37980.10591.4433-0.08080.05893.15640.51090.38061.02460.01110.932-13.7293-10.01449.5107
60.74940.36790.25020.38350.40060.18260.41710.1674-0.6883-0.18160.2605-0.26811.2230.1080.00013.09610.59340.32711.74950.01361.9777-4.1412-22.648133.4044
70.2008-0.0336-0.04960.04020.0939-0.0507-0.1815-0.9226-0.05231.2020.1714-0.62470.49450.2607-0.00672.40390.07710.07551.09230.25451.5191-14.3511-20.87375.9306
80.01680.3339-0.22930.37440.02671.04130.16180.0115-0.0533-0.1410.033-0.0297-0.0560.37440.00011.60110.12520.10331.36440.19481.23663.56258.569731.4036
90.27910.01770.1562-0.04430.33312.10450.1392-0.5806-0.05720.33250.0623-0.29930.4669-0.42540.00131.0714-0.2065-0.34271.69710.12771.030424.254352.2123103.5674
101.27281.2282-0.6991.1934-0.4859-0.76760.228-0.7463-0.23080.4537-0.4739-0.2659-0.14660.4522-0.00010.9046-0.14-0.06081.11360.15250.97017.662626.929784.6488
111.8622-0.2240.83190.80540.32440.23550.0515-0.4489-0.31190.87120.2873-1.92680.5190.20020.4022.2710.5055-0.73951.50640.10062.541353.016819.136384.0506
120.53750.44540.19020.54660.82630.88050.2875-0.5803-0.10370.90770.1172-0.60850.5389-0.0545-0.00012.6140.2874-0.7392.4190.29781.948548.355728.003113.6542
130.06510.34420.16430.37160.25560.0550.2933-1.0831-1.39640.6804-0.40220.3491-0.3445-0.26460.00011.3118-0.13580.04361.87250.30051.673138.146637.382165.584
140.9561-0.340.4030.14250.14460.62290.02360.7308-0.6598-0.09150.9432-0.02751.2925-1.89160.00022.4834-0.2761-0.32432.31110.39561.808120.789610.3725111.4364
151.63970.2250.95170.38881.16923.2576-0.0589-0.93370.02940.3804-0.01450.02390.4358-0.2393-0.00030.8609-0.0844-0.0871.46740.02560.8845-32.977833.6309114.0189
160.24920.2898-0.13910.21420.11060.33930.1475-0.2997-0.02020.2743-0.14530.0107-0.01420.084300.7691-0.1658-0.19930.9888-0.05650.9558-23.232357.037187.2665
171.3326-0.2167-0.24691.89150.87520.5562-0.0904-0.81060.04660.04970.03630.80370.1534-1.15580.02011.50410.65850.07961.8722-0.56741.6818-68.345760.3004109.968
180.11430.2355-0.2831.4565-0.5176-0.0402-0.1709-1.1006-0.09440.1576-0.0144-0.0098-0.0501-0.332101.43490.198-0.10883.1606-0.4681.1526-50.623647.4628142.2594
191.0604-1.4932-0.85121.48760.61180.4418-0.2156-0.22590.26360.06590.174-0.0708-1.3949-0.3270.02460.74180.0958-0.17811.6206-0.37311.104-68.254556.4141100.2052
201.66070.9404-0.28520.1483-0.3347-0.04550.2429-0.5480.3130.2832-0.27510.2845-0.1578-0.4788-01.1586-0.183-0.05561.436-0.35061.1849-35.650866.5325106.0644
211.67840.34570.41591.08070.92571.45910.09630.27380.0629-1.0693-0.19380.1216-0.6160.255-01.48470.1494-0.1690.7402-0.02291.0635-2.557571.484516.2816
221.97840.24741.58111.06321.03930.35390.0148-0.04850.14880.0034-0.1111-0.0742-0.0987-0.4240.00020.6675-0.0137-0.0620.5679-0.01570.89164.087474.965366.7027
230.97060.59570.51620.77271.47442.3246-0.10920.4143-0.0448-0.25860.1849-0.1019-0.2487-0.0071-00.7835-0.0169-0.11880.94420.00421.0062-34.07353.807144.2472
240.17020.03330.16810.3981-0.2580.19830.2828-0.46660.3192-0.4477-0.04980.24220.1035-0.2548-02.27340.2301-0.30361.3884-0.25111.8285-16.576108.422664.322
251.2741-0.0348-1.16570.8021-0.93430.50410.2330.74840.29-0.87640.29010.32290.18910.03760.00013.09050.5616-0.53421.42280.16431.887-16.9773104.00764.3038
260.15340.4307-0.41710.03450.250.3869-0.3587-0.2886-0.2148-2.5386-0.01110.0209-1.4447-0.10860.00583.21110.5228-1.04671.3136-0.00261.3701-15.773998.14859.1884
270.44940.1389-0.15090.1504-0.38850.477-0.1498-1.256-0.09221.11450.04111.284-2.2460.4997-0.02052.61340.8671-0.35761.7754-0.44842.5923-23.373107.87729.2268
280.09490.2947-0.01510.2749-0.16710.0503-0.15030.06080.5736-0.163-0.2782-0.5553-1.0971-0.51520.00023.113-0.3613-0.43361.4163-0.02092.3566-4.8792116.58959.0051
290.7893-0.42640.1760.313-0.28250.1212-0.0216-0.4311-0.76570.26480.5813-0.2499-1.38440.27470.0391.9555-0.3163-0.07171.0582-0.24191.0899-3.665499.428477.1453
300.6602-0.1488-0.46820.12-0.12560.6020.39690.3452-0.00670.4741-0.0094-0.05420.4028-0.323301.4919-0.0186-0.2150.98550.03771.3437-29.302979.238137.6724
31-0.0784-0.0442-0.03730.0976-0.14130.16370.30580.943-0.21640.33790.6075-0.2494-0.07030.6374-0.00021.56220.0051-0.18391.0187-0.05721.3418-46.768863.546415.9661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 356 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 357 THROUGH 639 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 640 THROUGH 1080 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 213 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 214 THROUGH 360 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 361 THROUGH 431 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 432 THROUGH 482 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 483 THROUGH 674 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 1 THROUGH 691 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 692 THROUGH 1080 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 1 THROUGH 114 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 115 THROUGH 464 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 465 THROUGH 552 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 553 THROUGH 674 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 1 THROUGH 662 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 663 THROUGH 1080 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 1 THROUGH 138 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 139 THROUGH 329 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 330 THROUGH 482 )
20X-RAY DIFFRACTION20CHAIN 'F' AND (RESID 483 THROUGH 674 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 1 THROUGH 595 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 596 THROUGH 805 )
23X-RAY DIFFRACTION23CHAIN 'G' AND (RESID 806 THROUGH 1080 )
24X-RAY DIFFRACTION24CHAIN 'H' AND (RESID 1 THROUGH 55 )
25X-RAY DIFFRACTION25CHAIN 'H' AND (RESID 56 THROUGH 213 )
26X-RAY DIFFRACTION26CHAIN 'H' AND (RESID 214 THROUGH 363 )
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 364 THROUGH 413 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 414 THROUGH 452 )
29X-RAY DIFFRACTION29CHAIN 'H' AND (RESID 453 THROUGH 497 )
30X-RAY DIFFRACTION30CHAIN 'H' AND (RESID 498 THROUGH 637 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 638 THROUGH 674 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more