[English] 日本語
Yorodumi
- PDB-4z5r: Rontalizumab Fab bound to Interferon-a2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z5r
TitleRontalizumab Fab bound to Interferon-a2
Components
  • Interferon alpha-2
  • anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
  • anti-IFN-a antibody rontalizumab light chain
KeywordsCytokine/Immune System / antibody / interferon / Cytokine-Immune System complex
Function / homology
Function and homology information


type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell ...type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / response to exogenous dsRNA / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling / B cell differentiation / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEigenbrot, C. / Maurer, B. / Bosanac, I.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural basis of the broadly neutralizing anti-interferon-alpha antibody rontalizumab.
Authors: Maurer, B. / Bosanac, I. / Shia, S. / Kwong, M. / Corpuz, R. / Vandlen, R. / Schmidt, K. / Eigenbrot, C.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Interferon alpha-2
J: anti-IFN-a antibody rontalizumab light chain
K: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
E: Interferon alpha-2
L: anti-IFN-a antibody rontalizumab light chain
M: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
F: Interferon alpha-2
V: anti-IFN-a antibody rontalizumab light chain
W: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
G: Interferon alpha-2
P: anti-IFN-a antibody rontalizumab light chain
Q: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
H: Interferon alpha-2
R: anti-IFN-a antibody rontalizumab light chain
S: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
I: Interferon alpha-2
T: anti-IFN-a antibody rontalizumab light chain
U: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
X: Interferon alpha-2
Y: anti-IFN-a antibody rontalizumab light chain
Z: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
N: Interferon alpha-2
A: anti-IFN-a antibody rontalizumab light chain
B: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,24632
Polymers539,47824
Non-polymers7698
Water00
1
D: Interferon alpha-2
J: anti-IFN-a antibody rontalizumab light chain
K: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6275
Polymers67,4353
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Interferon alpha-2
L: anti-IFN-a antibody rontalizumab light chain
M: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5314
Polymers67,4353
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Interferon alpha-2
V: anti-IFN-a antibody rontalizumab light chain
W: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7236
Polymers67,4353
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Interferon alpha-2
P: anti-IFN-a antibody rontalizumab light chain
Q: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6275
Polymers67,4353
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Interferon alpha-2
R: anti-IFN-a antibody rontalizumab light chain
S: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)


Theoretical massNumber of molelcules
Total (without water)67,4353
Polymers67,4353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
I: Interferon alpha-2
T: anti-IFN-a antibody rontalizumab light chain
U: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)


Theoretical massNumber of molelcules
Total (without water)67,4353
Polymers67,4353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
X: Interferon alpha-2
Y: anti-IFN-a antibody rontalizumab light chain
Z: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)


Theoretical massNumber of molelcules
Total (without water)67,4353
Polymers67,4353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
N: Interferon alpha-2
A: anti-IFN-a antibody rontalizumab light chain
B: anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)


Theoretical massNumber of molelcules
Total (without water)67,4353
Polymers67,4353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.829, 331.864, 98.142
Angle α, β, γ (deg.)90.00, 111.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21E
31F
41G
51H
61I
71X
81N
12J
22L
32V
42P
52R
62T
72A
82Y
13K
23M
33W
43Q
53S
63U
73B
83Z

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111D10 - 44
2111E10 - 44
3111F10 - 44
4111G10 - 44
5111H10 - 44
6111I10 - 44
7111X10 - 44
8111N10 - 44
1215D45 - 49
2215E45 - 49
3215F45 - 49
4215G45 - 49
5215H45 - 49
6215I45 - 49
7215X45 - 49
8215N45 - 49
1311D50 - 103
2311E50 - 103
3311F50 - 103
4311G50 - 103
5311H50 - 103
6311I50 - 103
7311X50 - 103
8311N50 - 103
1415D104 - 110
2415E104 - 110
3415F104 - 110
4415G104 - 110
5415H104 - 110
6415I104 - 110
7415X104 - 110
8415N104 - 110
1511D111 - 155
2511E111 - 155
3511F111 - 155
4511G111 - 155
5511H111 - 155
6511I111 - 155
7511X111 - 155
8511N111 - 155
1121J1 - 107
2121L1 - 107
3121V1 - 107
4121P1 - 107
5121R1 - 107
6121T1 - 107
7121A1 - 107
8121Y1 - 107
1221J108 - 213
2221L108 - 213
3221V108 - 213
4221P108 - 213
5221R108 - 213
6221T108 - 213
7221A108 - 213
8221Y108 - 213
1131K1 - 12
2131M1 - 12
3131W1 - 12
4131Q1 - 12
5131S1 - 12
6131U1 - 12
7131B1 - 12
8131Z1 - 12
1233K13
2233M13
3233W13
4233Q13
5233S13
6233U13
7233B13
8233Z13
1331K14 - 82
2331M14 - 82
3331W14 - 82
4331Q14 - 82
5331S14 - 82
6331U14 - 82
7331B14 - 82
8331Z14 - 82
1631K114 - 213
2631M114 - 213
3631W114 - 213
4631Q114 - 213
5631S114 - 213
6631U114 - 213
7631B114 - 213
8631Z114 - 213

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999858, 0.006989, -0.015336), (-0.006418, 0.999295, 0.037), (0.015584, -0.036896, 0.999198)-19.57423, 5.89448, 42.94949
3given(-0.999572, 0.028974, 0.004049), (-0.028168, -0.990547, 0.134254), (0.007901, 0.134082, 0.990939)43.69637, 8.30231, -1.54476
4given(-0.999957, 0.009009, -0.002111), (-0.009229, -0.98739, 0.158035), (-0.000661, 0.158047, 0.987431)63.8313, 9.37217, 40.40307
5given(-0.755257, 0.290552, -0.587508), (-0.301479, -0.949921, -0.082225), (-0.581977, 0.11502, 0.80503)43.20016, 82.18929, 6.53125
6given(-0.735596, -0.142001, 0.66237), (-0.303825, 0.943082, -0.135232), (-0.605466, -0.300721, -0.736871)-4.45551, -82.18892, 76.99711
7given(-0.717892, -0.157318, 0.678146), (-0.254158, 0.966119, -0.044931), (-0.648101, -0.204611, -0.733552)41.06792, -91.7597, 48.44725
8given(-0.73697, 0.324498, -0.592938), (-0.299031, -0.943234, -0.144535), (-0.606181, 0.070789, 0.79217)24.51319, 86.75475, 60.69896

-
Components

#1: Protein
Interferon alpha-2 / IFN-alpha-2 / Interferon alpha-A / LeIF A


Mass: 19264.096 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2, IFNA2A, IFNA2B, IFNA2C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01563
#2: Antibody
anti-IFN-a antibody rontalizumab light chain


Mass: 23855.402 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody
anti-IFN-a antibody rontalizumab heavy chain modules VH and CH1 (Fab)


Mass: 24315.209 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: lithium sulfate, PEG3350, 1% dioxane

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 109926 / Num. obs: 102259 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.095 / Net I/σ(I): 12.2

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVD
Resolution: 3→48.21 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.906 / SU B: 54.484 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25141 2285 2.2 %RANDOM
Rwork0.22264 ---
obs0.22329 99974 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.81 Å2
Baniso -1Baniso -2Baniso -3
1--10.95 Å20 Å21.5 Å2
2---5.65 Å20 Å2
3---12.29 Å2
Refinement stepCycle: LAST / Resolution: 3→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34016 0 40 0 34056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0234858
X-RAY DIFFRACTIONr_bond_other_d0.0040.0232289
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9547286
X-RAY DIFFRACTIONr_angle_other_deg0.9083.00274472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63554310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3524.1141485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.521155822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.98915165
X-RAY DIFFRACTIONr_chiral_restr0.0780.25264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02139218
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028055
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11D2125TIGHT THERMAL3.040.5
12E2125TIGHT THERMAL2.710.5
13F2125TIGHT THERMAL3.530.5
14G2125TIGHT THERMAL4.260.5
15H2125TIGHT THERMAL3.510.5
16I2125TIGHT THERMAL3.330.5
17X2125TIGHT THERMAL3.220.5
18N2125TIGHT THERMAL3.280.5
21J1611TIGHT THERMAL3.270.5
22L1611TIGHT THERMAL3.460.5
23V1611TIGHT THERMAL3.740.5
24P1611TIGHT THERMAL3.650.5
25R1611TIGHT THERMAL3.190.5
26T1611TIGHT THERMAL3.720.5
27A1611TIGHT THERMAL2.930.5
28Y1611TIGHT THERMAL3.840.5
31K19LOOSE POSITIONAL0.145
32M19LOOSE POSITIONAL0.265
33W19LOOSE POSITIONAL0.255
34Q19LOOSE POSITIONAL0.265
35S19LOOSE POSITIONAL0.175
36U19LOOSE POSITIONAL0.325
37B19LOOSE POSITIONAL0.45
38Z19LOOSE POSITIONAL0.315
31K1772TIGHT THERMAL3.720.5
32M1772TIGHT THERMAL2.710.5
33W1772TIGHT THERMAL2.750.5
34Q1772TIGHT THERMAL3.940.5
35S1772TIGHT THERMAL2.650.5
36U1772TIGHT THERMAL3.340.5
37B1772TIGHT THERMAL3.830.5
38Z1772TIGHT THERMAL3.410.5
31K19LOOSE THERMAL10.1110
32M19LOOSE THERMAL8.3510
33W19LOOSE THERMAL6.8410
34Q19LOOSE THERMAL3.6610
35S19LOOSE THERMAL3.1310
36U19LOOSE THERMAL7.5910
37B19LOOSE THERMAL4.5610
38Z19LOOSE THERMAL1.8710
LS refinement shellResolution: 3→3.206 Å
RfactorNum. reflection% reflection
Rfree1 0 0 %
Rwork0.294 15791 -
obs--81.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.2352-0.04830.58193.4818-2.05132.4251-0.23780.55740.1232-0.30440.15580.1731-0.252-0.01050.08190.9573-0.0227-0.02450.83680.17770.36383.859185.0159-13.2156
23.23981.0121-1.12716.7377-0.06351.8393-0.0123-0.4086-0.35890.25720.08950.14620.03450.1249-0.07710.8233-0.05580.0680.7250.20260.471248.824985.88870.7302
32.9066-2.2739-1.03553.66982.24363.5180.0024-0.3144-0.08690.12350.0053-0.15070.1439-0.1497-0.00770.61860.0085-0.0130.5502-0.01370.074715.512-9.384737.9104
43.0202-1.9549-0.24321.33130.17810.5647-0.088-0.0379-0.18850.0631-0.00870.20920.11120.0270.09670.6632-0.03550.09360.5094-0.04860.141424.6574-4.9784-4.8941
52.7996-1.47470.26521.7622-0.54540.2338-0.0067-0.1740.31410.1032-0.037-0.2694-0.06610.01980.04380.6914-0.0259-0.00950.5718-0.10120.171739.45511.905538
62.0614-2.54471.18585.6986-3.01874.25630.022-0.2950.10620.18160.0448-0.1969-0.16720.1818-0.06680.574-0.04880.04360.5278-0.03980.022448.538316.4629-6.0604
74.25620.6615-0.56655.3169-0.74491.93620.0002-0.35690.15840.3170.11420.1753-0.04710.0498-0.11430.7593-0.04270.06480.67830.28390.353930.37481.701448.3218
81.21271.1790.58353.799-2.10693.1474-0.00450.29220.0964-0.19540.21320.35880.0686-0.1111-0.20870.8683-0.0505-0.02831.0670.33230.4389-13.322377.17431.9579
910.4346-0.62172.67461.0016-0.92642.84680.1479-0.4260.20820.15450.00930.3007-0.0464-0.1666-0.15720.74060.00250.10370.349-0.14820.1952-11.911916.698440.253
1014.4894-2.68095.09542.2238-2.82745.2826-0.2069-0.58350.88880.26720.01840.2056-0.4309-0.4860.18850.75050.04890.10950.505-0.18140.26372.748615.9690.715
1113.8635-3.2687-5.70983.83721.6665.7967-0.2408-1.2015-0.8390.10180.0264-0.20880.43220.56940.21440.72820.0266-0.12380.59320.0860.385461.1969-8.83644.6255
129.50570.3796-2.59930.90290.9423.11510.0877-0.3327-0.18440.0777-0.0978-0.32720.05790.23950.01010.68940.0114-0.05510.41910.12040.213275.7273-9.7191-2.3171
137.0019-1.64513.45941.6773-0.76041.9973-0.2114-0.5888-0.96690.38770.4613-0.06420.33160.0532-0.24991.30770.04760.06231.03450.41870.932442.853248.880662.8505
145.7591.258-0.5451.52570.19220.9455-0.18360.26920.4138-0.24970.1017-0.022-0.00860.3660.0821.0842-0.0012-0.07091.04660.37240.5292-3.5819104.56727.6099
152.1462-2.10351.07172.1779-1.03060.5874-0.2069-0.478-0.65060.36770.47640.27790.078-0.0215-0.26951.63120.15880.17221.44460.47141.645559.129852.044614.0963
166.08351.1342-1.25522.001-0.81694.4029-0.08290.3347-0.0295-0.04370.134-0.2872-0.33810.1985-0.05110.9641-0.0458-0.01180.68850.19850.480825.102687.5281-5.9659
174.4526-1.99891.40443.6656-1.49262.79210.05680.1032-0.2072-0.17060.0659-0.5750.1720.3202-0.12270.9572-0.05390.10630.6312-0.00620.632469.492584.2956-8.6881
188.4154-1.54050.19182.54130.45012.01850.15680.2866-0.6144-0.1719-0.04210.18990.0955-0.0241-0.11470.7015-0.0037-0.04790.4491-0.07950.0975.4856-12.8918.0264
197.1362-2.57311.40131.79390.47131.5370.05080.562-0.444-0.1815-0.20660.26790.0573-0.02630.15570.7518-0.00860.01670.5508-0.16430.251224.7789-17.5489-25.9597
207.2616-1.63310.18772.4794-0.49832.79240.25860.39240.531-0.1567-0.2879-0.3607-0.08460.1810.02930.7010.03930.11810.51170.07010.247739.059423.067116.2289
219.1559-1.46780.08711.5545-0.29743.3240.05440.29660.1467-0.1152-0.1222-0.3005-0.11960.050.06780.6814-0.01320.1190.4420.02860.074658.517218.4229-26.1976
225.9348-2.48962.82583.543-3.51554.81740.1180.35770.1512-0.2234-0.0353-0.55260.07180.5023-0.08270.7817-0.04410.13070.74560.04890.52450.826380.956238.9018
235.38411.22-0.82981.4001-1.3173.03790.09330.14750.3954-0.03810.03630.0133-0.00260.0865-0.12960.8252-0.03430.01220.64120.2750.57967.299381.569640.1382
245.72873.04530.28696.74891.27571.2739-0.07590.20970.3433-0.1730.17660.4328-0.15550.1107-0.10070.6040.06340.03380.53810.06360.0747-6.528915.355124.6414
257.23233.98951.32034.37470.71841.1939-0.06680.31950.4049-0.04050.02620.4-0.08850.11220.04060.61060.00140.0770.5880.02230.048812.991710.2933-17.9312
265.90623.2815-0.84755.8208-0.72150.988-0.09290.2052-0.3779-0.04570.1311-0.53480.1467-0.1886-0.03810.63490.03550.01680.6014-0.07040.082751.0025-4.05425.8965
275.40483.5755-0.2534.3189-0.39091.2807-0.1570.3913-0.6143-0.19190.0803-0.40020.1009-0.10090.07670.610.0614-0.01340.6018-0.09050.160670.4706-8.9096-17.9266
287.88162.48631.67463.5663-0.09992.2869-0.18890.4146-0.9999-0.42660.24770.02360.6714-0.0798-0.05881.09260.0466-0.07150.84310.03760.910148.54451.036647.3318
298.7878-2.9285-0.03033.3827-0.48541.05920.0367-0.31751.16680.1421-0.4113-0.0834-0.6011-0.33590.37461.0592-0.0062-0.06921.12650.1670.83122.6921107.726122.8164
302.25992.4031-0.21783.31440.13581.5652-0.36650.3917-0.8178-0.12520.26680.06960.4739-0.25280.09981.4052-0.0336-0.03031.1981-0.00491.715164.886154.1674-1.6334
314.1865-1.00351.12664.73070.06993.0532-0.14680.2464-0.37-0.26080.09840.2640.1207-0.08780.04840.8138-0.04160.11470.61290.21580.605810.947963.00165.605
325.36320.7912-0.43057.63850.45143.44490.0331-0.4870.2240.19590.02120.27580.2664-0.0965-0.05420.8236-0.03820.0610.62640.18330.44156.6035111.937-11.928
333.56561.13730.15317.3880.08474.3168-0.04-0.2183-0.27880.2508-0.08140.1370.3543-0.1260.12140.63320.09650.01030.5549-0.08740.402826.5852-33.990124.418
343.55540.92361.17717.7460.53763.48410.066-0.1646-0.28370.2628-0.05050.46560.23-0.175-0.01550.67180.09660.10050.6092-0.1910.388746.1098-38.868-20.7284
355.38381.06890.25826.1066-0.64843.3913-0.02670.05840.35190.2590.0659-0.287-0.25990.0985-0.03910.65240.06380.1660.51140.08070.445118.329144.891519.8456
365.42790.815-0.24856.7602-1.00313.3463-0.0297-0.12610.16870.29-0.0186-0.2082-0.2090.00290.04830.62670.05940.11560.5180.03550.11236.741739.6296-22.5558
374.57060.89430.36147.99840.72633.27750.0607-0.23990.15350.15810.07830.0515-0.0908-0.1091-0.1390.7894-0.03270.08880.68430.31420.395436.8618107.626133.4854
384.5157-0.82530.5656.67520.48372.868-0.02070.48620.0002-0.25340.03890.26550.084-0.1148-0.01820.7248-0.05050.06910.68180.27370.3535-6.092157.006253.3202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Y1 - 106
2X-RAY DIFFRACTION2A1 - 107
3X-RAY DIFFRACTION3J1 - 107
4X-RAY DIFFRACTION4L1 - 107
5X-RAY DIFFRACTION5V1 - 107
6X-RAY DIFFRACTION6P1 - 107
7X-RAY DIFFRACTION7R1 - 107
8X-RAY DIFFRACTION8T1 - 107
9X-RAY DIFFRACTION9J108 - 213
10X-RAY DIFFRACTION10L108 - 213
11X-RAY DIFFRACTION11V108 - 213
12X-RAY DIFFRACTION12P108 - 213
13X-RAY DIFFRACTION13R108 - 213
14X-RAY DIFFRACTION14T108 - 213
15X-RAY DIFFRACTION15A108 - 213
16X-RAY DIFFRACTION16Z1 - 113
17X-RAY DIFFRACTION17B1 - 115
18X-RAY DIFFRACTION18K1 - 115
19X-RAY DIFFRACTION19M1 - 115
20X-RAY DIFFRACTION20W1 - 115
21X-RAY DIFFRACTION21Q1 - 115
22X-RAY DIFFRACTION22S1 - 115
23X-RAY DIFFRACTION23U1 - 115
24X-RAY DIFFRACTION24K116 - 213
25X-RAY DIFFRACTION25M116 - 213
26X-RAY DIFFRACTION26W116 - 213
27X-RAY DIFFRACTION27Q116 - 213
28X-RAY DIFFRACTION28S116 - 213
29X-RAY DIFFRACTION29U116 - 213
30X-RAY DIFFRACTION30B116 - 213
31X-RAY DIFFRACTION31X9 - 156
32X-RAY DIFFRACTION32N9 - 161
33X-RAY DIFFRACTION33D9 - 156
34X-RAY DIFFRACTION34E9 - 156
35X-RAY DIFFRACTION35F9 - 156
36X-RAY DIFFRACTION36G9 - 156
37X-RAY DIFFRACTION37H9 - 156
38X-RAY DIFFRACTION38I9 - 156

+
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://pdbjlvh1.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