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- PDB-4nen: An internal ligand-bound, metastable state of a leukocyte integri... -

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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


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / positive regulation of myelination / neutrophil migration ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / positive regulation of myelination / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / phagocytosis, engulfment / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / ECM proteoglycans / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / heat shock protein binding / cell adhesion molecule binding / receptor-mediated endocytosis / neutrophil chemotaxis / cell-matrix adhesion / secretory granule membrane / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / animal organ morphogenesis / microglial cell activation / receptor internalization / cell-cell adhesion / receptor tyrosine kinase binding / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular vesicle / integrin binding / cell-cell signaling / signaling receptor activity / amyloid-beta binding / regulation of cell shape / 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 / membrane / metal ion binding / 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 beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 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

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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 %

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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)

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  • 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

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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

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