[English] 日本語
Yorodumi
- PDB-4nen: An internal ligand-bound, metastable state of a leukocyte integri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nen
TitleAn internal ligand-bound, metastable state of a leukocyte integrin, aXb2
Components
  • Integrin alpha-X
  • Integrin beta-2
KeywordsCELL ADHESION / Complement receptor / iC3b / Fibrinogen / denaturated proteins / heparin / ICAM / N-linked Glycosylation / Membrane
Function / homology
Function and homology information


integrin alphaX-beta2 complex / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of endothelial tube morphogenesis / : / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade ...integrin alphaX-beta2 complex / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of endothelial tube morphogenesis / : / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / neutrophil migration / positive regulation of myelination / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / negative regulation of dopamine metabolic process / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / plasma membrane raft / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / positive regulation of protein targeting to membrane / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / specific granule membrane / positive regulation of superoxide anion generation / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / secretory granule membrane / animal organ morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor tyrosine kinase binding / receptor internalization / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / signaling receptor activity / regulation of cell shape / extracellular vesicle / 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 / positive regulation of cell population proliferation / apoptotic process / 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 tail domain / Integrin beta cytoplasmic domain ...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 tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / 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) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9012 Å
AuthorsSen, M. / Yuki, K. / Springer, T.A.
CitationJournal: J.Cell Biol. / Year: 2013
Title: An internal ligand-bound, metastable state of a leukocyte integrin, alpha X beta 2.
Authors: Sen, M. / Yuki, K. / Springer, T.A.
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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 2.2Oct 30, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,67916
Polymers196,2002
Non-polymers3,47914
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-23 kcal/mol
Surface area79650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.087, 119.851, 182.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#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: 120447.984 Da / Num. of mol.: 1 / Fragment: CD11c / Mutation: N42D, N368S, N678T, N885S and N920C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAX, CD11C / Plasmid: ET10 / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / 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: 75751.906 Da / Num. of mol.: 1 / Fragment: CD18 / Mutation: N190D, N232K and V696C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Plasmid: pef-puro / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: P05107

-
Sugars , 2 types, 6 molecules

#3: 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.: 5
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
#4: 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

-
Non-polymers , 4 types, 136 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 6% PEG 8000, 0.2 M Mg acetate, 0.1 M Na cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03329
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2011
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR AND K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03329 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 62271 / Num. obs: 61864 / % possible obs: 99.3 %

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K6S

3k6s


Resolution: 2.9012→47.809 Å / SU ML: 0.58 / σ(F): 1.99 / Phase error: 31.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 3117 5.04 %
Rwork0.2235 --
obs0.2255 61856 99.24 %
all-62271 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9012→47.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13325 0 220 128 13673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513983
X-RAY DIFFRACTIONf_angle_d0.76518982
X-RAY DIFFRACTIONf_dihedral_angle_d10.9685133
X-RAY DIFFRACTIONf_chiral_restr0.032135
X-RAY DIFFRACTIONf_plane_restr0.0032466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9012-2.94650.43621240.40812590X-RAY DIFFRACTION97
2.9465-2.99480.39141600.39612635X-RAY DIFFRACTION100
2.9948-3.04650.38941410.36882646X-RAY DIFFRACTION100
3.0465-3.10190.44281270.35522659X-RAY DIFFRACTION100
3.1019-3.16150.39221490.35012664X-RAY DIFFRACTION100
3.1615-3.2260.37461430.33882645X-RAY DIFFRACTION100
3.226-3.29620.35361380.32142634X-RAY DIFFRACTION100
3.2962-3.37280.32171500.29272647X-RAY DIFFRACTION100
3.3728-3.45710.35921550.2842669X-RAY DIFFRACTION100
3.4571-3.55060.32311430.27272673X-RAY DIFFRACTION100
3.5506-3.6550.28311320.25622656X-RAY DIFFRACTION100
3.655-3.7730.2671280.24262672X-RAY DIFFRACTION99
3.773-3.90780.26641390.23182668X-RAY DIFFRACTION100
3.9078-4.06410.2761520.20892670X-RAY DIFFRACTION100
4.0641-4.2490.22521430.18922672X-RAY DIFFRACTION100
4.249-4.47290.21211530.16752666X-RAY DIFFRACTION100
4.4729-4.75290.19271590.1572667X-RAY DIFFRACTION99
4.7529-5.11940.19851280.15362699X-RAY DIFFRACTION99
5.1194-5.63390.21281320.16982724X-RAY DIFFRACTION99
5.6339-6.44750.23561510.19512698X-RAY DIFFRACTION99
6.4475-8.11670.23141340.19742733X-RAY DIFFRACTION99
8.1167-47.81510.21361360.18232752X-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)
10.6706-0.2069-0.63840.49620.39080.8477-0.1680.0671-0.55920.29350.2023-0.55260.1570.14820.0050.50290.09210.07470.44770.07460.823-48.665111.18955.7419
21.0206-0.248-0.52961.4446-0.79181.72270.1928-0.01360.13960.1376-0.1427-0.3341-0.3018-0.066700.48580.05880.10250.75640.06590.8495-7.203225.522231.8371
30.0207-0.0282-0.03520.0540.04930.00790.2222-0.3612-0.2302-0.2265-0.5705-0.5429-0.46270.2605-0.00090.60660.00660.04410.54040.08390.5343-39.140537.808444.3347
41.0060.2192-0.39181.2395-0.25180.6784-0.18730.1402-0.14010.03230.20720.2716-0.0724-0.0904-00.43510.0340.03550.42030.03230.4403-65.122520.68549.0056
50.5845-0.09580.16720.4614-0.18381.03060.0408-0.3879-1.23820.24230.0398-0.13320.0836-0.28350.18610.7678-0.02410.27590.7750.39151.091-101.5483-5.215866.5308
60.8039-0.1288-0.25010.0481-0.30221.4273-0.6272-0.2222-0.2904-0.60390.41260.1340.5572-0.3923-0.02240.4864-0.05450.04530.94350.33420.7155-109.66728.322142.3506
71.02950.345-0.47630.1473-0.6521.5354-0.18190.0629-0.13720.01690.13120.11980.0103-0.0677-0.00010.6645-0.1468-0.0670.61490.09890.5411-79.1326.05494.8586
80.17040.14910.06150.40890.03340.3533-0.35620.23281.0734-0.0518-0.30980.17960.43990.2267-0.450.9992-0.00480.32281.24620.13841.4729-116.691435.190473.1277
91.4129-0.32260.25820.696-0.0410.2076-0.3272-0.41290.92080.64360.3780.20460.14280.0323-0.09950.66810.08030.38940.5179-0.04650.5343-76.025252.656471.7441
101.0598-0.5696-0.14341.47520.94020.6778-0.1055-0.09910.16450.47290.2228-0.24050.02370.06780.00010.50160.0844-0.02130.4311-0.0170.2857-51.977146.382864.5496
110.46480.4972-0.04770.03240.40330.06790.04930.23860.49580.5410.19620.5573-0.2264-0.1151-0.00120.63970.14570.17280.51290.10040.6309-82.334150.140368.6158
120.2436-0.0815-0.16240.06290.04760.12280.1488-0.40830.29390.5196-0.3620.35480.0401-0.3936-0.04961.34820.00290.7061.6314-0.16511.0232-118.84425.274486.4337
130.50330.03230.24770.23770.19341.4717-0.0287-0.16190.1569-0.36350.1069-0.08280.234-0.8230.12970.88140.13670.35171.20360.2581.3064-119.236914.701870.1683
140.0912-0.08630.05670.0798-0.02260.01170.459-0.31730.5063-0.2410.44890.4131-0.2770.53660.00181.2009-0.15330.48861.60620.27361.3052-99.101325.464857.628
15-0.0199-0.00070.0274-0.0255-0.03880.2169-0.44-0.7324-0.25350.799-1.0091-0.63550.4020.5414-0.02051.2711-0.42930.38140.95790.05961.626-86.522538.080839.5186
160.0139-0.00510.03260.0198-0.01010.09050.06840.30190.21440.26690.0070.01080.1550.00650.00031.2318-0.159-0.07480.7597-0.18921.5947-83.844233.502122.9114
170.38240.0127-0.14720.45080.50110.4039-0.08050.0383-0.190.0664-0.05460.5526-0.1632-0.31740.00020.8399-0.0609-0.02260.7137-0.17131.1877-78.831350.20714.7896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:124)
2X-RAY DIFFRACTION2chain 'A' and (resseq 129:310)
3X-RAY DIFFRACTION3chain 'A' and (resseq 311:334)
4X-RAY DIFFRACTION4chain 'A' and (resseq 336:596)
5X-RAY DIFFRACTION5chain 'A' and (resseq 600:750)
6X-RAY DIFFRACTION6chain 'A' and (resseq 758:902)
7X-RAY DIFFRACTION7chain 'A' and (resseq 903:1082)
8X-RAY DIFFRACTION8chain 'B' and (resseq 1:56)
9X-RAY DIFFRACTION9chain 'B' and (resseq 57:123)
10X-RAY DIFFRACTION10chain 'B' and (resseq 128:329)
11X-RAY DIFFRACTION11chain 'B' and (resseq 330:423)
12X-RAY DIFFRACTION12chain 'B' and (resseq 426:460)
13X-RAY DIFFRACTION13chain 'B' and (resseq 461:513)
14X-RAY DIFFRACTION14chain 'B' and (resseq 514:552)
15X-RAY DIFFRACTION15chain 'B' and (resseq 553:592)
16X-RAY DIFFRACTION16chain 'B' and (resseq 593:597)
17X-RAY DIFFRACTION17chain 'B' and (resseq 598:674)

+
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