PDB-4fmh: Merkel Cell Polyomavirus VP1 in complex with Disialyllactose

ID or keywords:

Entry

Database: PDB / ID: 4fmh

Title

Merkel Cell Polyomavirus VP1 in complex with Disialyllactose

Components

VP1

Keywords

VIRAL PROTEIN / viral capsid protein / jelly roll / encapsidation / receptor binding / sialylated oligosaccharides

Function / homology

Function and homology information

T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function

Biological species

Merkel cell polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Neu, U. / Hengel, H. / Stehle, T.

Citation

Journal: Plos Pathog. / Year: 2012
Title: Structures of Merkel Cell Polyomavirus VP1 Complexes Define a Sialic Acid Binding Site Required for Infection.
Authors: Neu, U. / Hengel, H. / Blaum, B.S. / Schowalter, R.M. / Macejak, D. / Gilbert, M. / Wakarchuk, W.W. / Imamura, A. / Ando, H. / Kiso, M. / Arnberg, N. / Garcea, R.L. / Peters, T. / Buck, C.B. / Stehle, T.

History

Deposition	Jun 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: 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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 2.1	Nov 20, 2024	Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fmh.cif.gz	2.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4fmh.ent.gz	1.8 MB	Display	PDB format
PDBx/mmJSON format	4fmh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fmh_validation.pdf.gz	1006 KB	Display	wwPDB validaton report
Full document	4fmh_full_validation.pdf.gz	1 MB	Display
Data in XML	4fmh_validation.xml.gz	273.5 KB	Display
Data in CIF	4fmh_validation.cif.gz	365.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fm/4fmh ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fmh	HTTPS FTP

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Related structure data

Related structure data	4fmgC 4fmiC 4fmjC C: citing same article (ref.)
Similar structure data	4fmi-2 4fmi-1 4fmj-3 1cn3-d 4fmj-4 6y5x-2 6y67-2 4por-2 4fmj-1 4fmi-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4fmgC

4fmiC

4fmjC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (5)

Deposited unit

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

648 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

hetero molecules

defined by author&software
161 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

defined by author&software
163 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

defined by author&software
162 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

K: VP1

L: VP1

M: VP1

N: VP1

O: VP1

hetero molecules

defined by software
324 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

P: VP1

Q: VP1

R: VP1

S: VP1

T: VP1

hetero molecules

defined by software
324 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.270, 85.770, 248.710
Angle α, β, γ (deg.)	92.97, 100.48, 108.05
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	ALA	ALA	A	A	96 - 100	65 - 69
2	1	GLU	GLU	ALA	ALA	B	B	96 - 100	65 - 69
3	1	GLU	GLU	ALA	ALA	C	C	96 - 100	65 - 69
4	1	GLU	GLU	ALA	ALA	D	D	96 - 100	65 - 69
5	1	GLU	GLU	ALA	ALA	E	E	96 - 100	65 - 69
6	1	GLU	GLU	ALA	ALA	F	F	96 - 100	65 - 69
7	1	GLU	GLU	ALA	ALA	G	G	96 - 100	65 - 69
8	1	GLU	GLU	ALA	ALA	H	H	96 - 100	65 - 69
9	1	GLU	GLU	ALA	ALA	I	I	96 - 100	65 - 69
10	1	GLU	GLU	ALA	ALA	J	J	96 - 100	65 - 69
11	1	GLU	GLU	ALA	ALA	K	K	96 - 100	65 - 69
12	1	GLU	GLU	ALA	ALA	L	L	96 - 100	65 - 69
13	1	GLU	GLU	ALA	ALA	M	M	96 - 100	65 - 69
14	1	GLU	GLU	ALA	ALA	N	N	96 - 100	65 - 69
15	1	GLU	GLU	ALA	ALA	O	O	96 - 100	65 - 69
16	1	GLU	GLU	ALA	ALA	P	P	96 - 100	65 - 69
17	1	GLU	GLU	ALA	ALA	Q	Q	96 - 100	65 - 69
18	1	GLU	GLU	ALA	ALA	R	R	96 - 100	65 - 69
19	1	GLU	GLU	ALA	ALA	S	S	96 - 100	65 - 69
20	1	GLU	GLU	ALA	ALA	T	T	96 - 100	65 - 69
1	2	TRP	TRP	TYR	TYR	A	A	123 - 143	92 - 112
2	2	TRP	TRP	TYR	TYR	B	B	123 - 143	92 - 112
3	2	TRP	TRP	TYR	TYR	C	C	123 - 143	92 - 112
4	2	TRP	TRP	TYR	TYR	D	D	123 - 143	92 - 112
5	2	TRP	TRP	TYR	TYR	E	E	123 - 143	92 - 112
6	2	TRP	TRP	TYR	TYR	F	F	123 - 143	92 - 112
7	2	TRP	TRP	TYR	TYR	G	G	123 - 143	92 - 112
8	2	TRP	TRP	TYR	TYR	H	H	123 - 143	92 - 112
9	2	TRP	TRP	TYR	TYR	I	I	123 - 143	92 - 112
10	2	TRP	TRP	TYR	TYR	J	J	123 - 143	92 - 112
11	2	TRP	TRP	TYR	TYR	K	K	123 - 143	92 - 112
12	2	TRP	TRP	TYR	TYR	L	L	123 - 143	92 - 112
13	2	TRP	TRP	TYR	TYR	M	M	123 - 143	92 - 112
14	2	TRP	TRP	TYR	TYR	N	N	123 - 143	92 - 112
15	2	TRP	TRP	TYR	TYR	O	O	123 - 143	92 - 112
16	2	TRP	TRP	TYR	TYR	P	P	123 - 143	92 - 112
17	2	TRP	TRP	TYR	TYR	Q	Q	123 - 143	92 - 112
18	2	TRP	TRP	TYR	TYR	R	R	123 - 143	92 - 112
19	2	TRP	TRP	TYR	TYR	S	S	123 - 143	92 - 112
20	2	TRP	TRP	TYR	TYR	T	T	123 - 143	92 - 112
1	3	ALA	ALA	TYR	TYR	A	A	167 - 182	136 - 151
2	3	ALA	ALA	TYR	TYR	B	B	167 - 182	136 - 151
3	3	ALA	ALA	TYR	TYR	C	C	167 - 182	136 - 151
4	3	ALA	ALA	TYR	TYR	D	D	167 - 182	136 - 151
5	3	ALA	ALA	TYR	TYR	E	E	167 - 182	136 - 151
6	3	ALA	ALA	TYR	TYR	F	F	167 - 182	136 - 151
7	3	ALA	ALA	TYR	TYR	G	G	167 - 182	136 - 151
8	3	ALA	ALA	TYR	TYR	H	H	167 - 182	136 - 151
9	3	ALA	ALA	TYR	TYR	I	I	167 - 182	136 - 151
10	3	ALA	ALA	TYR	TYR	J	J	167 - 182	136 - 151
11	3	ALA	ALA	TYR	TYR	K	K	167 - 182	136 - 151
12	3	ALA	ALA	TYR	TYR	L	L	167 - 182	136 - 151
13	3	ALA	ALA	TYR	TYR	M	M	167 - 182	136 - 151
14	3	ALA	ALA	TYR	TYR	N	N	167 - 182	136 - 151
15	3	ALA	ALA	TYR	TYR	O	O	167 - 182	136 - 151
16	3	ALA	ALA	TYR	TYR	P	P	167 - 182	136 - 151
17	3	ALA	ALA	TYR	TYR	Q	Q	167 - 182	136 - 151
18	3	ALA	ALA	TYR	TYR	R	R	167 - 182	136 - 151
19	3	ALA	ALA	TYR	TYR	S	S	167 - 182	136 - 151
20	3	ALA	ALA	TYR	TYR	T	T	167 - 182	136 - 151
1	4	PRO	PRO	SER	SER	A	A	227 - 236	196 - 205
2	4	PRO	PRO	SER	SER	B	B	227 - 236	196 - 205
3	4	PRO	PRO	SER	SER	C	C	227 - 236	196 - 205
4	4	PRO	PRO	SER	SER	D	D	227 - 236	196 - 205
5	4	PRO	PRO	SER	SER	E	E	227 - 236	196 - 205
6	4	PRO	PRO	SER	SER	F	F	227 - 236	196 - 205
7	4	PRO	PRO	SER	SER	G	G	227 - 236	196 - 205
8	4	PRO	PRO	SER	SER	H	H	227 - 236	196 - 205
9	4	PRO	PRO	SER	SER	I	I	227 - 236	196 - 205
10	4	PRO	PRO	SER	SER	J	J	227 - 236	196 - 205
11	4	PRO	PRO	SER	SER	K	K	227 - 236	196 - 205
12	4	PRO	PRO	SER	SER	L	L	227 - 236	196 - 205
13	4	PRO	PRO	SER	SER	M	M	227 - 236	196 - 205
14	4	PRO	PRO	SER	SER	N	N	227 - 236	196 - 205
15	4	PRO	PRO	SER	SER	O	O	227 - 236	196 - 205
16	4	PRO	PRO	SER	SER	P	P	227 - 236	196 - 205
17	4	PRO	PRO	SER	SER	Q	Q	227 - 236	196 - 205
18	4	PRO	PRO	SER	SER	R	R	227 - 236	196 - 205
19	4	PRO	PRO	SER	SER	S	S	227 - 236	196 - 205
20	4	PRO	PRO	SER	SER	T	T	227 - 236	196 - 205
1	5	GLY	GLY	PRO	PRO	A	A	272 - 275	241 - 244
2	5	GLY	GLY	PRO	PRO	B	B	272 - 275	241 - 244
3	5	GLY	GLY	PRO	PRO	C	C	272 - 275	241 - 244
4	5	GLY	GLY	PRO	PRO	D	D	272 - 275	241 - 244
5	5	GLY	GLY	PRO	PRO	E	E	272 - 275	241 - 244
6	5	GLY	GLY	PRO	PRO	F	F	272 - 275	241 - 244
7	5	GLY	GLY	PRO	PRO	G	G	272 - 275	241 - 244
8	5	GLY	GLY	PRO	PRO	H	H	272 - 275	241 - 244
9	5	GLY	GLY	PRO	PRO	I	I	272 - 275	241 - 244
10	5	GLY	GLY	PRO	PRO	J	J	272 - 275	241 - 244
11	5	GLY	GLY	PRO	PRO	K	K	272 - 275	241 - 244
12	5	GLY	GLY	PRO	PRO	L	L	272 - 275	241 - 244
13	5	GLY	GLY	PRO	PRO	M	M	272 - 275	241 - 244
14	5	GLY	GLY	PRO	PRO	N	N	272 - 275	241 - 244
15	5	GLY	GLY	PRO	PRO	O	O	272 - 275	241 - 244
16	5	GLY	GLY	PRO	PRO	P	P	272 - 275	241 - 244
17	5	GLY	GLY	PRO	PRO	Q	Q	272 - 275	241 - 244
18	5	GLY	GLY	PRO	PRO	R	R	272 - 275	241 - 244
19	5	GLY	GLY	PRO	PRO	S	S	272 - 275	241 - 244
20	5	GLY	GLY	PRO	PRO	T	T	272 - 275	241 - 244
1	6	ILE	ILE	PHE	PHE	A	A	284 - 294	253 - 263
2	6	ILE	ILE	PHE	PHE	B	B	284 - 294	253 - 263
3	6	ILE	ILE	PHE	PHE	C	C	284 - 294	253 - 263
4	6	ILE	ILE	PHE	PHE	D	D	284 - 294	253 - 263
5	6	ILE	ILE	PHE	PHE	E	E	284 - 294	253 - 263
6	6	ILE	ILE	PHE	PHE	F	F	284 - 294	253 - 263
7	6	ILE	ILE	PHE	PHE	G	G	284 - 294	253 - 263
8	6	ILE	ILE	PHE	PHE	H	H	284 - 294	253 - 263
9	6	ILE	ILE	PHE	PHE	I	I	284 - 294	253 - 263
10	6	ILE	ILE	PHE	PHE	J	J	284 - 294	253 - 263
11	6	ILE	ILE	PHE	PHE	K	K	284 - 294	253 - 263
12	6	ILE	ILE	PHE	PHE	L	L	284 - 294	253 - 263
13	6	ILE	ILE	PHE	PHE	M	M	284 - 294	253 - 263
14	6	ILE	ILE	PHE	PHE	N	N	284 - 294	253 - 263
15	6	ILE	ILE	PHE	PHE	O	O	284 - 294	253 - 263
16	6	ILE	ILE	PHE	PHE	P	P	284 - 294	253 - 263
17	6	ILE	ILE	PHE	PHE	Q	Q	284 - 294	253 - 263
18	6	ILE	ILE	PHE	PHE	R	R	284 - 294	253 - 263
19	6	ILE	ILE	PHE	PHE	S	S	284 - 294	253 - 263
20	6	ILE	ILE	PHE	PHE	T	T	284 - 294	253 - 263
1	7	HIS	HIS	ARG	ARG	A	A	303 - 307	272 - 276
2	7	HIS	HIS	ARG	ARG	B	B	303 - 307	272 - 276
3	7	HIS	HIS	ARG	ARG	C	C	303 - 307	272 - 276
4	7	HIS	HIS	ARG	ARG	D	D	303 - 307	272 - 276
5	7	HIS	HIS	ARG	ARG	E	E	303 - 307	272 - 276
6	7	HIS	HIS	ARG	ARG	F	F	303 - 307	272 - 276
7	7	HIS	HIS	ARG	ARG	G	G	303 - 307	272 - 276
8	7	HIS	HIS	ARG	ARG	H	H	303 - 307	272 - 276
9	7	HIS	HIS	ARG	ARG	I	I	303 - 307	272 - 276
10	7	HIS	HIS	ARG	ARG	J	J	303 - 307	272 - 276
11	7	HIS	HIS	ARG	ARG	K	K	303 - 307	272 - 276
12	7	HIS	HIS	ARG	ARG	L	L	303 - 307	272 - 276
13	7	HIS	HIS	ARG	ARG	M	M	303 - 307	272 - 276
14	7	HIS	HIS	ARG	ARG	N	N	303 - 307	272 - 276
15	7	HIS	HIS	ARG	ARG	O	O	303 - 307	272 - 276
16	7	HIS	HIS	ARG	ARG	P	P	303 - 307	272 - 276
17	7	HIS	HIS	ARG	ARG	Q	Q	303 - 307	272 - 276
18	7	HIS	HIS	ARG	ARG	R	R	303 - 307	272 - 276
19	7	HIS	HIS	ARG	ARG	S	S	303 - 307	272 - 276
20	7	HIS	HIS	ARG	ARG	T	T	303 - 307	272 - 276
1	8	VAL	VAL	ARG	ARG	A	A	311 - 316	280 - 285
2	8	VAL	VAL	ARG	ARG	B	B	311 - 316	280 - 285
3	8	VAL	VAL	ARG	ARG	C	C	311 - 316	280 - 285
4	8	VAL	VAL	ARG	ARG	D	D	311 - 316	280 - 285
5	8	VAL	VAL	ARG	ARG	E	E	311 - 316	280 - 285
6	8	VAL	VAL	ARG	ARG	F	F	311 - 316	280 - 285
7	8	VAL	VAL	ARG	ARG	G	G	311 - 316	280 - 285
8	8	VAL	VAL	ARG	ARG	H	H	311 - 316	280 - 285
9	8	VAL	VAL	ARG	ARG	I	I	311 - 316	280 - 285
10	8	VAL	VAL	ARG	ARG	J	J	311 - 316	280 - 285
11	8	VAL	VAL	ARG	ARG	K	K	311 - 316	280 - 285
12	8	VAL	VAL	ARG	ARG	L	L	311 - 316	280 - 285
13	8	VAL	VAL	ARG	ARG	M	M	311 - 316	280 - 285
14	8	VAL	VAL	ARG	ARG	N	N	311 - 316	280 - 285
15	8	VAL	VAL	ARG	ARG	O	O	311 - 316	280 - 285
16	8	VAL	VAL	ARG	ARG	P	P	311 - 316	280 - 285
17	8	VAL	VAL	ARG	ARG	Q	Q	311 - 316	280 - 285
18	8	VAL	VAL	ARG	ARG	R	R	311 - 316	280 - 285
19	8	VAL	VAL	ARG	ARG	S	S	311 - 316	280 - 285
20	8	VAL	VAL	ARG	ARG	T	T	311 - 316	280 - 285

#1: Protein

VP1

Mass: 31927.154 Da / Num. of mol.: 20 / Fragment: UNP residues 37-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Merkel cell polyomavirus / Strain: W162 / Gene: VP1 / Production host:

Escherichia coli (E. coli) / References: UniProt: C0JPK1

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose

Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2	WURCS	PDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}	LINUCS	PDB-CARE

#3: Chemical

...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Chemical

ChemComp-CL / CHLORIDE ION

Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 4560 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.5 % Description: THE CRYSTAL SUFFERED FROM RADIATION DAMAGE DURING DATA COLLECTION.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate, pH 6.5, 6% w/v PEG3350, 0.3 M magnesium chloride, soaked in 20 mM disialyllactose, cryoprotection: 25% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2010
Radiation	Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. all: 558787 / Num. obs: 529047 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / R_merge(I) obs: 0.096 / Net I/σ(I): 9.52
Reflection shell	Resolution: 1.85→1.9 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.612 / Mean I/σ(I) obs: 1.74 / % possible all: 90

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Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.946 / SU B: 5.203 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE BINDING SITES IN CHAINS E AND S CONTAIN ONLY VERY WEAK ELECTRON DENSITY FEATURES FOR THE LIGAND. RESIDUES 71 AND 72 ADOPT MULTIPLE CONFORMATIONS IN THE STRUCTURE.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19575	5310	1 %	RANDOM
R_work	0.16564	-	-	-
obs	0.16595	523737	94.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.148 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.66 Å²	0.28 Å²	-0.05 Å²
2-	-	0.31 Å²	-0.15 Å²
3-	-	-	-0.83 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42808	0	580	4560	47948

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	45469
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.108	1.983	62120
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.923	5	5709
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.519	25.113	1858
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.676	15	7467
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.296	15	164
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	6998
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	34363
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.019	3	28130
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.855	5	46049
X-RAY DIFFRACTION	r_scbond_it	2.755	7	17339
X-RAY DIFFRACTION	r_scangle_it	4.27	9	16055
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	312	medium positional	0.05	0.5
2	B	312	medium positional	0.05	0.5
3	C	312	medium positional	0.09	0.5
4	D	312	medium positional	0.05	0.5
5	E	312	medium positional	0.06	0.5
6	F	312	medium positional	0.08	0.5
7	G	312	medium positional	0.05	0.5
8	H	312	medium positional	0.05	0.5
9	I	312	medium positional	0.07	0.5
10	J	312	medium positional	0.05	0.5
11	K	312	medium positional	0.06	0.5
12	L	312	medium positional	0.05	0.5
13	M	312	medium positional	0.06	0.5
14	N	312	medium positional	0.07	0.5
15	O	312	medium positional	0.06	0.5
16	P	312	medium positional	0.05	0.5
17	Q	312	medium positional	0.05	0.5
18	R	312	medium positional	0.06	0.5
19	S	312	medium positional	0.05	0.5
20	T	312	medium positional	0.04	0.5
1	A	283	loose positional	0.08	5
2	B	283	loose positional	0.09	5
3	C	283	loose positional	0.12	5
4	D	283	loose positional	0.09	5
5	E	283	loose positional	0.09	5
6	F	283	loose positional	0.12	5
7	G	283	loose positional	0.08	5
8	H	283	loose positional	0.08	5
9	I	283	loose positional	0.1	5
10	J	283	loose positional	0.08	5
11	K	283	loose positional	0.08	5
12	L	283	loose positional	0.08	5
13	M	283	loose positional	0.09	5
14	N	283	loose positional	0.1	5
15	O	283	loose positional	0.09	5
16	P	283	loose positional	0.09	5
17	Q	283	loose positional	0.08	5
18	R	283	loose positional	0.1	5
19	S	283	loose positional	0.07	5
20	T	283	loose positional	0.07	5
1	A	312	medium thermal	0.5	2
2	B	312	medium thermal	0.46	2
3	C	312	medium thermal	0.51	2
4	D	312	medium thermal	0.54	2
5	E	312	medium thermal	0.53	2
6	F	312	medium thermal	0.87	2
7	G	312	medium thermal	0.52	2
8	H	312	medium thermal	0.42	2
9	I	312	medium thermal	0.53	2
10	J	312	medium thermal	0.79	2
11	K	312	medium thermal	0.57	2
12	L	312	medium thermal	0.52	2
13	M	312	medium thermal	0.71	2
14	N	312	medium thermal	0.55	2
15	O	312	medium thermal	0.68	2
16	P	312	medium thermal	0.69	2
17	Q	312	medium thermal	0.53	2
18	R	312	medium thermal	0.77	2
19	S	312	medium thermal	0.63	2
20	T	312	medium thermal	0.48	2
1	A	283	loose thermal	0.56	10
2	B	283	loose thermal	0.53	10
3	C	283	loose thermal	0.55	10
4	D	283	loose thermal	0.59	10
5	E	283	loose thermal	0.59	10
6	F	283	loose thermal	0.75	10
7	G	283	loose thermal	0.57	10
8	H	283	loose thermal	0.52	10
9	I	283	loose thermal	0.58	10
10	J	283	loose thermal	0.68	10
11	K	283	loose thermal	0.56	10
12	L	283	loose thermal	0.62	10
13	M	283	loose thermal	0.65	10
14	N	283	loose thermal	0.56	10
15	O	283	loose thermal	0.67	10
16	P	283	loose thermal	0.71	10
17	Q	283	loose thermal	0.63	10
18	R	283	loose thermal	0.67	10
19	S	283	loose thermal	0.66	10
20	T	283	loose thermal	0.54	10

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.299	395	-
R_work	0.26	36818	-
obs	-	-	89.77 %

Refinement TLS params.

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

ID	L11 (°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)
1	8.269	-4.3016	4.3309	5.5642	-2.9661	7.2878	0.1422	0.5141	0.2984	-0.3094	-0.3521	-0.1634	-0.1498	0.3686	0.21	0.1542	-0.0706	0.0191	0.1057	0.0254	0.0671	11.875	28.266	-25.583
2	0.3555	-0.0191	0.0403	0.4675	-0.0109	0.5343	-0.0033	-0.0081	0.0798	-0.0165	-0.0288	-0.0254	-0.1093	0.1133	0.0321	0.0295	-0.0321	-0.0051	0.0722	-0.0022	0.0535	13.278	20.419	2.065
3	1.6019	-0.3226	1.5893	3.203	-2.3592	5.7785	0.0565	0.1634	-0.0422	-0.39	-0.101	-0.1845	0.518	0.3669	0.0446	0.0853	0.0314	0.0634	0.1314	-0.0119	0.1103	23.496	-10.503	-20.242
4	0.5317	0.0835	0.0621	0.5388	0.0091	0.4052	-0.0271	0.0371	0.0157	-0.0817	0.0173	-0.0761	-0.0037	0.1472	0.0097	0.0203	0.0141	0.0181	0.1034	0.004	0.0599	23.108	-4.266	-7.832
5	6.0754	0.539	-3.6766	3.4614	-1.6402	12.025	-0.0409	0.6459	0.0979	-0.1675	0.1455	0.0951	0.0521	-0.8518	-0.1045	0.1309	0.0104	-0.0384	0.1175	-0.0347	0.0891	-10.368	-22.005	-31.583
6	0.3667	0.0103	0.0107	0.3402	0.0254	0.6042	-0.0024	0.0135	-0.0857	-0.0409	-0.0072	-0.0405	0.1531	0.0411	0.0095	0.0579	0.0179	0.0141	0.0366	0.0065	0.0657	1.246	-24.559	-6.171
7	1.815	1.2309	0.3827	4.6087	5.1671	15.213	-0.0849	0.0334	0.1251	-0.5568	-0.2058	0.274	-0.9011	-0.6015	0.2906	0.1146	0.0441	-0.0635	0.1912	0.0079	0.171	-34.657	-1.345	-19.64
8	0.3472	0.0189	0.0104	0.4183	0.0515	0.5575	-0.0056	-0.0075	-0.0353	-0.0176	-0.0288	0.0598	0.0477	-0.0927	0.0344	0.0072	-0.0077	0.0077	0.0475	-0.007	0.0426	-21.841	-10.261	4.414
9	7.3295	0.7469	5.8165	1.8966	0.5271	7.6513	-0.382	0.4394	0.2992	-0.1902	0.0738	0.0007	-0.424	0.1984	0.3082	0.201	0.0239	-0.0159	0.137	0.0219	0.1818	-20.477	29.703	-14.854
10	0.4745	0.0615	0.0463	0.4296	0.011	0.5408	-0.0224	-0.0308	0.0666	0.01	-0.015	0.0696	-0.0746	-0.0462	0.0374	0.0216	0.0074	-0.0018	0.0309	-0.0238	0.0469	-14.698	17.26	9.134
11	8.8126	1.9497	4.468	3.493	2.7514	10.1773	-0.5455	0.5411	0.174	-0.2007	0.3809	0.0364	-0.7171	-0.0804	0.1646	0.2343	0.0517	-0.0442	0.1313	0.0304	0.0895	14.57	5.162	-139.075
12	0.5181	-0.0047	0.1446	0.4487	-0.0347	0.5716	-0.0589	-0.0424	0.0651	0.0553	0.015	0.0822	-0.1558	-0.1133	0.0438	0.0783	0.0465	-0.0022	0.0391	-0.0162	0.0344	21.195	-5.012	-113.097
13	2.0529	-0.8442	1.8187	1.1523	-1.0095	4.0859	-0.0604	0.2141	0.2003	-0.0285	-0.1365	-0.1319	-0.0704	0.4285	0.197	0.1002	-0.0635	-0.0009	0.081	0.02	0.1146	56.628	-1.111	-129.795
14	0.3792	-0.0486	0.1136	0.4742	-0.0322	0.679	-0.0401	0.0285	0.0878	0.0166	-0.0117	-0.0203	-0.163	0.0411	0.0518	0.0903	-0.0181	-0.0232	0.0509	-0.0022	0.0495	47.796	-2.334	-120.691
15	2.6275	0.1207	0.5118	8.4328	-6.4007	10.125	-0.164	0.2574	-0.0063	-0.8017	0.0869	-0.0245	0.6817	0.2015	0.0772	0.1428	-0.0081	0.0514	0.1497	-0.0145	0.047	54.112	-29.932	-155.497
16	0.5578	0.0777	0.095	0.5713	-0.0722	0.5865	-0.0284	0.0604	0.0034	-0.0474	0.0105	-0.0824	0.0332	0.1687	0.018	0.0502	0.0208	0.0097	0.0901	-0.0016	0.0646	59.289	-28.687	-127.95
17	3.8787	0.6878	-2.1701	2.2269	-1.7279	12.5418	-0.1549	0.4869	-0.0005	-0.2092	0.1523	0.0351	0.6032	-0.6796	0.0025	0.1539	-0.0245	-0.0224	0.0855	-0.0229	0.0583	25.297	-47.976	-149.136
18	0.4515	-0.0169	0.0344	0.4597	0.0194	0.6369	-0.0025	0.0207	-0.0816	-0.0095	0.0072	-0.0274	0.1749	0.0079	-0.0047	0.1013	0.0083	0.0096	0.0238	0.0085	0.0583	37.24	-47.509	-124.018
19	2.4088	1.217	0.3241	6.1383	3.6366	13.1455	-0.0068	0.1385	0.1601	-0.8564	-0.2797	0.4049	-0.9717	-1.1065	0.2865	0.1497	0.092	-0.0591	0.2002	0.0195	0.1223	0.993	-25.359	-140.137
20	0.4689	0.0245	0.0608	0.5336	0.026	0.6644	-0.0134	-0.0484	-0.0493	0.0209	0.0031	0.0894	0.0555	-0.1851	0.0104	0.0303	-0.0017	0.026	0.0701	0.01	0.0397	13.818	-32.906	-115.491
21	4.8051	1.8121	5.1736	5.366	4.1035	12.2114	0.2776	-0.4273	-0.224	0.5141	-0.1079	-0.207	0.4454	-0.6447	-0.1697	0.1899	-0.0035	0.0351	0.1855	0.0204	0.1141	-37.115	19.532	-30.941
22	0.3837	-0.0059	0.1162	0.5464	0.054	0.567	-0.0023	-0.0577	0.0445	0.0088	-0.0305	0.0502	-0.1178	-0.1465	0.0328	0.0633	0.0363	-0.0123	0.0616	-0.0175	0.0499	-38.728	28.152	-58.105
23	3.4677	-0.6128	-0.5807	2.2869	1.1871	13.1957	-0.0429	-0.2416	-0.0777	0.1518	0.1726	-0.0748	0.7668	0.3068	-0.1296	0.1716	-0.0408	-0.0089	0.0953	0.0547	0.0986	-31.142	-11.958	-40.535
24	0.3711	-0.0306	-0.0059	0.3669	0.053	0.4306	-0.0098	-0.0272	-0.0307	-0.0002	-0.0108	0.0662	0.0609	-0.1133	0.0205	0.0523	-0.0132	-0.0083	0.0549	-0.015	0.0476	-37.554	0.268	-65.641
25	2.9535	2.1467	-0.3693	4.1888	-4.1174	8.8219	0.1981	-0.3605	-0.144	0.2225	-0.4758	-0.2238	-0.0563	0.7606	0.2777	0.1995	0.0572	-0.0153	0.1518	0.0046	0.1793	2.13	-13.266	-51.372
26	0.3402	0.0271	0.0426	0.4399	-0.062	0.5655	0.0162	0.0004	-0.0613	-0.0357	-0.0213	-0.0279	0.1101	0.0341	0.0052	0.0722	0.0091	0.0063	0.0199	-0.0099	0.0474	-10.539	-6.122	-74.006
27	2.9618	-2.9954	2.4421	8.174	-4.5119	5.3653	-0.1647	-0.1185	0.0882	0.5825	0.063	-0.2264	-0.3825	0.1555	0.1018	0.1128	-0.0402	-0.0002	0.1945	-0.014	0.1557	15.797	17.683	-47.737
28	0.462	-0.1098	0.0755	0.4429	-0.029	0.734	-0.0062	0.0078	-0.0042	-0.0507	-0.0029	-0.1108	-0.061	0.1198	0.0092	0.0671	-0.0275	0.0258	0.0526	0.0005	0.0728	5.334	18.513	-72.45
29	10.3595	-3.7191	5.9522	2.3222	-3.6596	12.1016	-0.4405	-1.0832	-0.1232	0.2517	0.3518	-0.0966	-0.5162	-0.5485	0.0887	0.1691	-0.0011	-0.017	0.1322	0.0083	0.063	-8.721	38.514	-35.642
30	0.4583	-0.0406	-0.0149	0.4357	0.0313	0.5087	0.0022	-0.0301	0.0438	-0.0587	-0.0035	-0.0687	-0.205	0.037	0.0013	0.1182	-0.0113	0.0052	0.0054	-0.0037	0.0244	-12.492	39.686	-62.93
31	0.6883	-0.2481	0.3255	0.9104	0.3544	5.5663	0.036	-0.0641	-0.0627	0.0717	-0.0404	0.0773	0.4896	-0.0362	0.0043	0.1134	-0.0596	0.0108	0.1313	0.0125	0.1612	0.758	-38.85	-180.609
32	0.5114	-0.0738	0.0332	0.4063	0.0585	0.5297	0.0077	-0.0501	-0.0376	0.058	-0.0055	0.0639	0.0611	-0.0881	-0.0023	0.0425	-0.0272	-0.0034	0.0813	0.0021	0.0727	-1.899	-27.629	-185.1
33	1.59	0.4148	-0.0286	3.1804	-2.3329	9.5164	0.1744	-0.3064	0.0028	0.3173	-0.3253	-0.1929	0.0426	0.9391	0.151	0.2095	0.0152	-0.0535	0.1694	0.0244	0.1606	38.64	-40.669	-169.811
34	0.4299	0.064	0.0423	0.4616	-0.0213	0.5402	0.0254	0.0092	-0.0913	-0.0026	-0.0154	-0.0095	0.112	0.0236	-0.0101	0.0392	0.005	-0.007	0.0533	-0.0077	0.0585	24.974	-35.091	-194.719
35	2.6235	-1.9159	2.4639	5.6819	-4.584	5.0994	-0.1044	-0.1602	0.1061	0.4889	-0.0238	-0.1189	-0.4669	0.1622	0.1282	0.1548	-0.0199	-0.0134	0.2216	-0.012	0.1549	51.541	-9.605	-169.894
36	0.4136	-0.0387	0.0589	0.3869	-0.0764	0.6317	0.0004	0.0268	-0.0065	-0.0104	-0.0112	-0.0852	0.0051	0.1113	0.0109	0.0179	-0.014	0.0122	0.0793	0.0068	0.0684	41.127	-10.931	-194.583
37	10.7659	-2.3507	6.2852	3.7402	-2.1862	7.588	-0.2422	-0.6048	0.0702	0.2853	0.0977	-0.0448	-0.3731	-0.2739	0.1444	0.2151	-0.0292	0.0098	0.134	-0.0458	0.1039	27.408	11.98	-158.652
38	0.4469	0.0356	0.0515	0.347	-0.0407	0.4679	-0.0053	-0.0153	0.0829	0.0189	-0.0008	-0.0354	-0.113	0.0216	0.0062	0.0375	-0.0096	0.0047	0.0272	0.0103	0.0578	23.265	11.048	-187.079
39	5.5025	1.9564	5.0769	4.8928	4.3385	11.0104	0.2805	-0.3554	-0.214	0.5224	-0.1402	-0.1349	0.4418	-0.5497	-0.1404	0.137	-0.0021	0.055	0.1358	0.0271	0.0788	-1.271	-6.048	-153.457
40	0.4147	-0.0093	0.0171	0.4403	0.014	0.3989	0.0146	-0.0241	0.0753	0.0473	-0.0167	0.0413	-0.0678	-0.1096	0.0021	0.0242	0.01	0.0102	0.0634	0.0087	0.0598	-2.893	0.115	-181.384

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	40 - 56
2	X-RAY DIFFRACTION	2	A	57 - 319
3	X-RAY DIFFRACTION	3	B	40 - 73
4	X-RAY DIFFRACTION	4	B	74 - 319
5	X-RAY DIFFRACTION	5	C	40 - 56
6	X-RAY DIFFRACTION	6	C	57 - 319
7	X-RAY DIFFRACTION	7	D	40 - 56
8	X-RAY DIFFRACTION	8	D	57 - 320
9	X-RAY DIFFRACTION	9	E	40 - 57
10	X-RAY DIFFRACTION	10	E	58 - 320
11	X-RAY DIFFRACTION	11	F	40 - 56
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