[English] 日本語
Yorodumi
- PDB-6z3m: Repulsive Guidance Molecule B (RGMB) in complex with Growth Diffe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z3m
TitleRepulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).
Components
  • Growth/differentiation factor 5
  • Neogenin
  • RGM domain family member B
KeywordsSIGNALING PROTEIN / Repulsive Guidance Molecule / RGM / Bone Morphogenetic Protein / BMP / Growth Differentiation Factor 5 / GDF5 / Neogenin / axon guidance / TGFbeta signalling / brain development / iron metabolism
Function / homology
Function and homology information


ossification involved in bone remodeling / trans-synaptic signaling, modulating synaptic transmission / forelimb morphogenesis / chondroblast differentiation / BMP binding / hindlimb morphogenesis / negative regulation of axon regeneration / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation ...ossification involved in bone remodeling / trans-synaptic signaling, modulating synaptic transmission / forelimb morphogenesis / chondroblast differentiation / BMP binding / hindlimb morphogenesis / negative regulation of axon regeneration / negative regulation of mesenchymal cell apoptotic process / Netrin-1 signaling / positive regulation of chondrocyte differentiation / co-receptor binding / mesenchymal cell apoptotic process / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / endoplasmic reticulum-Golgi intermediate compartment / intracellular vesicle / protein secretion / positive regulation of SMAD protein signal transduction / regulation of multicellular organism growth / negative regulation of protein secretion / chondrocyte differentiation / response to mechanical stimulus / BMP signaling pathway / coreceptor activity / side of membrane / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / postsynaptic density membrane / multicellular organismal-level iron ion homeostasis / negative regulation of epithelial cell proliferation / cell-cell signaling / signaling receptor activity / growth cone / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / cell adhesion / cadherin binding / membrane raft / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / glutamatergic synapse / cell surface / Golgi apparatus / signal transduction / extracellular space / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminal domain / Repulsive guidance molecule (RGM) N-terminal domain / Neogenin, C-terminal / Neogenin C-terminus / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site ...Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminal domain / Repulsive guidance molecule (RGM) N-terminal domain / Neogenin, C-terminal / Neogenin C-terminus / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Growth/differentiation factor 5 / Neogenin / Repulsive guidance molecule B
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.501 Å
AuthorsMalinauskas, T. / Peer, T.V. / Bishop, B. / Muller, T.D. / Siebold, C.
Funding support United Kingdom, European Union, Germany, France, 7items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council (ERC)647278European Union
German Research Foundation (DFG)MU1095/3-2 Germany
German Research Foundation (DFG)MU1095/5-1 Germany
Wellcome Trust203852/Z/16/2 United Kingdom
Human Frontier Science Program (HFSP)LT000021/2014-L France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Repulsive guidance molecules lock growth differentiation factor 5 in an inhibitory complex.
Authors: Malinauskas, T. / Peer, T.V. / Bishop, B. / Mueller, T.D. / Siebold, C.
History
DepositionMay 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 24, 2023Group: Database references / Structure summary / Category: chem_comp / database_2 / struct
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.5Jul 26, 2023Group: Author supporting evidence / Other / Category: pdbx_audit_support / pdbx_database_status
Item: _pdbx_audit_support.country / _pdbx_database_status.pdb_format_compatible
Revision 1.6Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Growth/differentiation factor 5
B: Growth/differentiation factor 5
C: RGM domain family member B
D: RGM domain family member B
E: Neogenin
F: Neogenin
G: Growth/differentiation factor 5
H: Growth/differentiation factor 5
I: RGM domain family member B
J: RGM domain family member B
K: Neogenin
L: Neogenin
M: Growth/differentiation factor 5
N: Growth/differentiation factor 5
O: RGM domain family member B
P: RGM domain family member B
Q: Neogenin
R: Neogenin
c: RGM domain family member B
d: RGM domain family member B
i: RGM domain family member B
j: RGM domain family member B
o: RGM domain family member B
p: RGM domain family member B
S: RGM domain family member B
T: RGM domain family member B
U: RGM domain family member B
V: RGM domain family member B
W: RGM domain family member B
X: RGM domain family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)989,27439
Polymers987,28430
Non-polymers1,9919
Water00
1
A: Growth/differentiation factor 5
B: Growth/differentiation factor 5
C: RGM domain family member B
D: RGM domain family member B
E: Neogenin
F: Neogenin
c: RGM domain family member B
d: RGM domain family member B
S: RGM domain family member B
T: RGM domain family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,75813
Polymers329,09510
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Growth/differentiation factor 5
H: Growth/differentiation factor 5
I: RGM domain family member B
J: RGM domain family member B
K: Neogenin
L: Neogenin
i: RGM domain family member B
j: RGM domain family member B
U: RGM domain family member B
V: RGM domain family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,75813
Polymers329,09510
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: Growth/differentiation factor 5
N: Growth/differentiation factor 5
O: RGM domain family member B
P: RGM domain family member B
Q: Neogenin
R: Neogenin
o: RGM domain family member B
p: RGM domain family member B
W: RGM domain family member B
X: RGM domain family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,75813
Polymers329,09510
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)279.480, 279.480, 142.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein
Growth/differentiation factor 5 / GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 ...GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 / Lipopolysaccharide-associated protein 4 / LPS-associated protein 4 / Radotermin


Mass: 13405.481 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43026
#2: Protein
RGM domain family member B / DRG11-responsive axonal guidance and outgrowth of neurite / DRAGON


Mass: 41036.719 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: Sequence alignment is misleading. / Source: (gene. exp.) Homo sapiens (human) / Gene: RGMB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6NW40
#3: Protein
Neogenin


Mass: 28031.631 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neo1, Ngn / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P97798
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000 / PH range: 6.7-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 5.5→70.19 Å / Num. obs: 20764 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.253 / Net I/σ(I): 5.7
Reflection shellResolution: 5.5→5.64 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1499 / CC1/2: 0.278 / Rpim(I) all: 1.103

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z3J

6z3j


Resolution: 5.501→69.87 Å / SU ML: 2.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 61.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4282 1061 5.13 %
Rwork0.3257 --
obs0.331 20690 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.501→69.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25084 0 126 0 25210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01225781
X-RAY DIFFRACTIONf_angle_d1.48935040
X-RAY DIFFRACTIONf_dihedral_angle_d15.2849509
X-RAY DIFFRACTIONf_chiral_restr0.114003
X-RAY DIFFRACTIONf_plane_restr0.0074479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.501-5.7510.48911380.4292412X-RAY DIFFRACTION100
5.751-6.05410.43981410.43352440X-RAY DIFFRACTION100
6.0541-6.43320.46831300.42342441X-RAY DIFFRACTION100
6.4332-6.92950.46931140.39952471X-RAY DIFFRACTION100
6.9295-7.6260.48181380.36222449X-RAY DIFFRACTION100
7.626-8.72770.40061470.31652447X-RAY DIFFRACTION100
8.7277-10.98910.37911290.26792468X-RAY DIFFRACTION100
10.9891-69.870.43321240.2872501X-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)
13.37081.44340.43035.37082.55381.23841.5862-2.33163.7477-0.13771.4373-1.92370.88584.6171.42936.7733-2.74331.02322.9315-1.37883.9921-86.353360.0825-49.0632
22.20321.66151.27376.4573-4.6046.46033.05-1.199-1.3581-2.5359-1.0729-2.16075.24293.38151.67396.0427-0.2422-0.3622.0623-0.20184.616-95.727746.8803-52.7452
30.6821-0.8602-0.07651.24460.38553.1109-0.21820.36680.80030.1550.3394-1.20871.95793.1519-1.90267.6196-3.3079-2.13448.686-2.89640.8333-80.761962.3918-72.4917
44.6389-2.97240.69434.5286-4.99917.3378-0.26146.2847-1.2702-0.7644-2.0278-1.55870.0342.5268-3.57018.4683-1.8265-3.70747.7379-1.162.769-89.752336.7849-31.0677
58.3986-0.91622.78012.98353.07815.01431.298-0.8361-0.89662.96731.82861.47892.4652-4.1962-0.97146.5125-1.11623.15326.35510.74257.96576.532955.03240.9143
60.4745-1.236-1.0972.99643.01533.0205-5.1123.0281-1.11463.64171.50243.81590.158-1.78811.41738.3522-0.21481.21284.39081.00215.9011-9.433654.528844.7777
72.37681.60490.59230.97760.31120.08340.89550.46411.5946-0.3482-1.49162.5769-4.5669-2.6558-5.94595.03722.37682.31448.1808-3.89534.884511.920865.431362.5068
88.43940.6564-1.38093.0359-1.67411.02814.13540.2413-1.7579-1.351.923-2.05591.0233-0.37756.10167.5586-3.0592-1.11798.6855-3.65452.8672-15.185656.68121.7393
95.7041.2945-5.17175.03941.06386.1744-1.03581.3276-0.62120.69751.33121.63560.61855.4722-0.38262.5833-0.2556-0.18575.58690.71434.4663-132.625325.223349.4315
104.1788-4.15760.43597.6818-3.66466.3649-0.1019-1.28-2.49761.3203-0.4130.6019-1.0076-1.52990.6121.89320.5917-0.97985.4667-1.5475.6813-148.830125.370445.7152
116.38280.39151.69195.8408-2.12481.3233-4.76750.11-4.26192.1899-0.37611.30443.4682-7.35971.53245.9628-0.95461.97457.7394-0.25493.9825-127.422916.030927.7049
127.34190.41697.01518.68293.12667.6204-0.0629-4.3852-1.96212.79613.4150.20450.17860.4904-1.15082.8322-0.24890.75536.9085-1.9134.6342-154.116521.098269.399
133.55793.4888-2.1727.8084-3.50017.9433-3.82723.2987-4.0562-1.37222.2891-2.52141.12031.21920.44043.1303-2.07990.65055.3399-0.46942.2979-51.5028108.1154-60.4394
142.8768-0.18340.95172.87990.5250.533-1.286-0.86040.00121.5826-0.97532.1725-1.7199-0.5495-0.53875.9613-2.68542.42334.7354-2.20172.735-89.6949113.4077-39.0899
150.7699-0.8898-2.13537.4208-0.81437.77650.8073-2.00691.84180.210.5141-6.12243.30961.238-0.9612.7621-0.3201-0.04282.8573-0.91415.1905-122.3601-5.1213-41.9146
160.08230.0457-1.00544.80320.2217.9315-0.09712.7104-2.1526-1.3653-2.18291.5420.6698-1.04831.67814.03190.175-0.69682.3714-1.43186.5074-147.07228.8298-55.4192
172.35341.914-2.06711.3227-1.43451.57541.7486-3.7225-0.88461.1807-0.22381.6776-1.2222-0.4851-0.66755.66883.74032.60068.66841.1037.397565.122658.392453.7267
188.53015.3444.67586.24440.4434.47270.73530.5169-4.6186-4.06281.0773-2.31641.53730.0192-1.50127.40032.8571.38677.5280.01165.821347.845820.621739.105
198.72514.2911-4.21764.85871.5096.80991.9879-2.4589-2.4399-1.9318-2.5409-2.7269-0.5469-1.56021.25827.6538-3.08392.48136.6973-1.32785.2256-68.077761.58334.4133
201.3526-0.17523.4496-0.0099-0.34138.2413-2.51880.44810.47210.03-0.9852-0.8609-2.45-2.78411.33845.9082-1.37482.74917.5617-2.66959.2019-51.90329.095156.5649
215.61710.9048-5.68828.2477-0.87066.94731.37483.193.0545-2.35760.24382.73031.2897-1.4069-1.15813.27-0.3549-1.32394.7387-0.04283.9758-72.995721.100137.0254
221.85920.6630.29435.8123-0.76573.8562-1.2284-3.67842.4463.51871.77432.27941.8199-0.06593.00451.84040.20710.94184.7005-1.663-1.2862-89.39659.314251.754
232.4345-1.775-0.86246.30587.5041.96785.05874.8675-1.01131.858-1.0811-2.14725.2014-0.3089-1.85994.94370.1369-1.20727.8998-1.1975.9097-206.175822.390653.5726
242.6343-0.952-1.62010.43470.78021.04441.3341.55241.0094-0.61790.8032-0.08121.7981-2.80821.68924.06370.1802-3.87299.5745-0.07885.8293-189.970460.228938.0324
252.036-0.6615-0.1378.54080.48883.461-1.3225-1.308-0.54972.0732.00892.52173.5885-0.49660.52126.4577-2.89273.07922.7408-1.37556.1429-83.226693.9878-47.8338
269.2401-4.2194.57578.0876-4.30314.18624.16471.82956.06651.3931-4.0659-0.0981-1.88391.7434-0.47113.19370.27250.43742.42090.93497.3023-125.210430.45-51.662
275.15596.11670.52867.4989-0.95554.00853.2924-1.8868-3.76253.7338-4.13880.0714-2.6806-4.9850.4785.61871.65830.43996.66931.76716.162235.68138.123444.7577
280.0421-0.0698-0.13070.09070.47911.17981.8367-1.72551.28280.48024.5669-0.50040.3655-1.873-2.40375.2959-1.7639-1.50126.82511.222511.501-39.838543.355349.5957
296.0941-3.6959-2.84615.5658-1.58444.92610.74932.9707-3.5356-2.9663-2.00312.68255.0561-4.97380.52283.9169-1.5591-1.14464.90190.0193.9375-101.995342.070646.2478
303.77012.6291-3.28719.76551.24124.25750.1183.1789-1.572.3953-0.6289-0.70080.40960.64130.29862.4881.3304-0.58028.05831.36647.0692-177.2542.706543.0237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 397 through 501)
2X-RAY DIFFRACTION2(chain 'B' and resid 396 through 501)
3X-RAY DIFFRACTION3(chain 'C' and resid 53 through 127)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 127)
5X-RAY DIFFRACTION5(chain 'G' and resid 396 through 501)
6X-RAY DIFFRACTION6(chain 'H' and resid 397 through 501)
7X-RAY DIFFRACTION7(chain 'I' and resid 1 through 127)
8X-RAY DIFFRACTION8(chain 'J' and resid 53 through 126)
9X-RAY DIFFRACTION9(chain 'M' and resid 397 through 501)
10X-RAY DIFFRACTION10(chain 'N' and resid 396 through 501)
11X-RAY DIFFRACTION11(chain 'O' and resid 53 through 127)
12X-RAY DIFFRACTION12(chain 'P' and resid 1 through 127)
13X-RAY DIFFRACTION13(chain 'E' and resid 884 through 983)
14X-RAY DIFFRACTION14(chain 'E' and resid 984 through 1088)
15X-RAY DIFFRACTION15(chain 'F' and resid 884 through 983)
16X-RAY DIFFRACTION16(chain 'F' and resid 984 through 1088)
17X-RAY DIFFRACTION17(chain 'K' and resid 884 through 983)
18X-RAY DIFFRACTION18(chain 'K' and resid 984 through 1088)
19X-RAY DIFFRACTION19(chain 'L' and resid 884 through 983)
20X-RAY DIFFRACTION20(chain 'L' and resid 984 through 1088)
21X-RAY DIFFRACTION21(chain 'Q' and resid 884 through 983)
22X-RAY DIFFRACTION22(chain 'Q' and resid 984 through 1088)
23X-RAY DIFFRACTION23(chain 'R' and resid 884 through 983)
24X-RAY DIFFRACTION24(chain 'R' and resid 984 through 1088)
25X-RAY DIFFRACTION25(chain 'c' and resid 138 through 321)
26X-RAY DIFFRACTION26(chain 'd' and resid 138 through 321)
27X-RAY DIFFRACTION27(chain 'i' and resid 138 through 321)
28X-RAY DIFFRACTION28(chain 'j' and resid 138 through 321)
29X-RAY DIFFRACTION29(chain 'o' and resid 138 through 321)
30X-RAY DIFFRACTION30(chain 'p' and resid 138 through 321)

+
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