[English] 日本語
Yorodumi
- PDB-3v4v: crystal structure of a4b7 headpiece complexed with Fab ACT-1 and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v4v
Titlecrystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376
Components
  • (MONOCLONAL ANTIBODY Act-1 ...) x 2
  • Integrin alpha-4
  • Integrin beta-7
KeywordsCELL ADHESION / MAdCAM-1 / Membrane
Function / homology
Function and homology information


clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / T cell migration ...clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / T cell migration / positive regulation of leukocyte tethering or rolling / axonogenesis involved in innervation / protein antigen binding / leukocyte tethering or rolling / RUNX3 Regulates Immune Response and Cell Migration / positive regulation of endothelial cell apoptotic process / heterotypic cell-cell adhesion / integrin complex / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / neuron projection extension / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / receptor clustering / endodermal cell differentiation / cellular response to cytokine stimulus / fibronectin binding / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / B cell differentiation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / virus receptor activity / growth cone / Potential therapeutics for SARS / receptor complex / cell adhesion / external side of plasma membrane / focal adhesion / neuronal cell body / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...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 alpha Ig-like domain 3 / 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) / EGF-like domain, extracellular / EGF-like domain / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-0DU / Integrin alpha-4 / Integrin beta-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYu, Y. / Zhu, J. / Springer, T.A.
CitationJournal: J.Cell Biol. / Year: 2012
Title: Structural specializations of a4b7, an Integrin that Mediates Rolling Adhesion
Authors: Yu, Y. / Zhu, J. / Mi, L.Z. / Walz, T. / Sun, H. / Chen, J. / Springer, T.A.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_formal_charge / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-4
B: Integrin beta-7
H: MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN
L: MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN
C: Integrin alpha-4
D: Integrin beta-7
M: MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN
N: MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,63436
Polymers337,0778
Non-polymers5,55728
Water55831
1
A: Integrin alpha-4
B: Integrin beta-7
H: MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN
L: MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,48919
Polymers168,5394
Non-polymers2,95015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-4
D: Integrin beta-7
M: MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN
N: MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,14517
Polymers168,5394
Non-polymers2,60713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.580, 123.530, 154.160
Angle α, β, γ (deg.)90.00, 112.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 1:430
211chain C and resid 1:430
112chain A and resid 432:470
212chain C and resid 432:470
113chain A and resid 480:560
213chain C and resid 480:560
114chain B and resid 133:371
214chain D and resid 133:371
115chain B and (resid 80:126 or resid 373:454)
215chain D and (resid 80:126 or resid 373:454)
116chain M and resid 1:120
216chain H and resid 1:120
117chain M and resid 121:200
217chain H and resid 121:200
118chain N and resid 1:111
218chain L and resid 1:111
119chain N and resid 112:215
219chain L and resid 112:215

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin alpha-4 / CD49 antigen-like family member D / Integrin alpha-IV / VLA-4 subunit alpha


Mass: 65644.656 Da / Num. of mol.: 2 / Fragment: unp residues 34-620 / Mutation: R558A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA4, CD49D / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P13612
#2: Protein Integrin beta-7 / Gut homing receptor beta subunit


Mass: 55426.227 Da / Num. of mol.: 2 / Fragment: unp residues 20-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB7 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P26010

-
Antibody , 2 types, 4 molecules HMLN

#3: Antibody MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN


Mass: 23570.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Antibody MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN


Mass: 23897.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

-
Sugars , 2 types, 13 molecules

#5: 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
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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 , 5 types, 46 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-0DU / N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine


Mass: 527.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H19Cl2F3N2O4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.1 M NaCl, 8-10% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03337 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2009
RadiationMonochromator: double silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03337 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 286405 / Num. obs: 79083 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.1→3.2634 Å / % possible all: 97

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1034 1.31 %
Rwork0.1971 --
obs0.1976 79033 98.44 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.854 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.8083 Å20 Å21.2887 Å2
2--13.2309 Å2-0 Å2
3----17.9524 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21394 0 344 31 21769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522296
X-RAY DIFFRACTIONf_angle_d0.79130268
X-RAY DIFFRACTIONf_dihedral_angle_d13.1868173
X-RAY DIFFRACTIONf_chiral_restr0.0513355
X-RAY DIFFRACTIONf_plane_restr0.0033916
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3288X-RAY DIFFRACTIONPOSITIONAL
12C3288X-RAY DIFFRACTIONPOSITIONAL0.071
21A298X-RAY DIFFRACTIONPOSITIONAL
22C298X-RAY DIFFRACTIONPOSITIONAL0.022
31A590X-RAY DIFFRACTIONPOSITIONAL
32C590X-RAY DIFFRACTIONPOSITIONAL0.015
41B1853X-RAY DIFFRACTIONPOSITIONAL
42D1853X-RAY DIFFRACTIONPOSITIONAL0.011
51B1006X-RAY DIFFRACTIONPOSITIONAL
52D1006X-RAY DIFFRACTIONPOSITIONAL0.009
61M941X-RAY DIFFRACTIONPOSITIONAL
62H941X-RAY DIFFRACTIONPOSITIONAL0.042
71M535X-RAY DIFFRACTIONPOSITIONAL
72H535X-RAY DIFFRACTIONPOSITIONAL0.011
81N851X-RAY DIFFRACTIONPOSITIONAL
82L851X-RAY DIFFRACTIONPOSITIONAL0.01
91N811X-RAY DIFFRACTIONPOSITIONAL
92L811X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.26340.34641500.305810934X-RAY DIFFRACTION97
3.2634-3.46790.33661450.265111004X-RAY DIFFRACTION98
3.4679-3.73560.29561480.227311098X-RAY DIFFRACTION98
3.7356-4.11140.23711380.203111195X-RAY DIFFRACTION99
4.1114-4.70610.18741640.152211182X-RAY DIFFRACTION99
4.7061-5.92820.20381240.179111284X-RAY DIFFRACTION99
5.9282-56.66640.20151650.180911302X-RAY DIFFRACTION98
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)
12.00970.53730.20812.12640.22922.009-0.02870.017-0.2974-0.072-0.005-0.28030.05260.56770.01260.41190.0418-0.03150.75190.03440.372812.197227.078743.2027
21.02480.41851.83121.58130.82715.5818-0.0684-0.40790.05170.19580.12360.08790.25810.268-0.06910.7776-0.0832-0.05671.67970.01290.605341.181243.676977.8444
32.8858-0.6544-0.1091.34330.07963.692-0.0528-0.1906-0.3420.1867-0.04820.41240.1308-0.46920.08240.5629-0.09780.04160.51580.00720.4306-21.303728.000753.3748
43.75750.67410.46034.03630.18454.0877-0.3983-0.54730.4290.61650.1818-0.4022-0.46860.35210.13361.2923-0.01350.06181.4138-0.15880.5807-12.988941.225482.8632
54.4567-1.5669-1.27243.77761.32012.73460.14880.21710.6618-0.089-0.12690.2351-0.55-0.1615-0.0280.8360.3791-0.03870.89010.00480.7275-44.699871.86433.1425
62.58860.8119-1.86124.11910.26261.54810.3204-0.30820.3710.242-0.46190.198-0.6376-0.05470.04981.13940.1039-0.11360.7856-0.20040.6597-52.578868.593868.6422
72.4577-0.0191-0.47592.1129-1.17284.9326-0.08020.10010.0711-0.1026-0.0580.1342-0.1481-0.49940.1320.55720.2132-0.00650.6611-0.09630.6738-40.243251.180536.5997
84.532-1.7915-0.32524.17980.10933.580.18270.0333-0.3204-0.066-0.14080.5591-0.227-0.5909-0.07380.6826-0.0021-0.00070.9793-0.22540.711-61.844255.040365.7092
91.8771-0.4748-0.21121.9385-0.40162.9496-0.01110.21280.3618-0.0811-0.0054-0.1974-0.39750.2320.00130.6815-0.1327-0.01750.75380.060.41098.953763.40588.8776
102.6299-1.4151-2.31563.50720.13345.77010.02210.577-0.6721-0.49050.00690.298-0.2810.36850.03730.93560.0099-0.04851.31970.05650.758938.581446.0258-24.8733
111.28910.56610.02320.81390.39013.7327-0.06410.24510.1783-0.0679-0.00170.3411-0.174-0.78040.05260.84890.1394-0.10111.03670.15840.5583-24.326557.151-0.3807
123.0626-0.82610.01462.87840.19814.8229-0.25050.2207-0.08030.08460.0495-0.13590.1379-0.00370.09110.8766-0.1708-0.17691.44920.0830.4207-15.348445.1985-30.509
133.53892.18751.7014.26260.66084.3284-0.05880.5183-0.4986-0.50780.11670.52940.3896-0.2463-0.08980.6326-0.015-0.07320.7839-0.26950.7778-41.160510.364821.5824
142.3253-0.7710.68030.7689-1.27393.60860.26620.6555-0.006-1.4505-0.09040.0463-0.68240.36440.00012.7105-0.3112-0.45321.9168-0.15411.0428-51.589111.2741-12.814
153.98190.24110.53275.7254-2.1334.633-0.09130.87080.1839-0.8587-0.07350.569-0.0851-0.60950.19710.64440.0621-0.12860.8406-0.1830.6759-39.590731.445517.3414
161.36050.589-0.38511.8069-0.69651.1321-0.68480.2020.7623-0.94450.36811.26640.1407-0.05990.29891.8652-0.2303-0.72112.103-0.21271.4587-62.498823.9118-9.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:430
2X-RAY DIFFRACTION2chain A and resid 431:587
3X-RAY DIFFRACTION3chain B and resid 131:371
4X-RAY DIFFRACTION4chain B and (resid 81:130 or resid 372:458)
5X-RAY DIFFRACTION5chain M and resid 1:121
6X-RAY DIFFRACTION6chain M and resid 122:219
7X-RAY DIFFRACTION7chain N and resid 1:112
8X-RAY DIFFRACTION8chain N and resid 113:215
9X-RAY DIFFRACTION9chain C and resid 1:430
10X-RAY DIFFRACTION10chain C and resid 431:587
11X-RAY DIFFRACTION11chain D and resid 131:371
12X-RAY DIFFRACTION12chain D and (resid 81:130 or resid 372:458)
13X-RAY DIFFRACTION13chain H and resid 1:121
14X-RAY DIFFRACTION14chain H and resid 122:218
15X-RAY DIFFRACTION15chain L and resid 1:112
16X-RAY DIFFRACTION16chain L and resid 113:215

+
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