PDB-4ln8: The crystal structure of hemagglutinin from a h7n9 influenza viru...

ID or keywords:

Entry

Database: PDB / ID: 4ln8

Title

The crystal structure of hemagglutinin from a h7n9 influenza virus (a/shanghai/2/2013) in complex with lstb

Components

(Hemagglutinin) x 2

Keywords

VIRAL PROTEIN / RECEPTOR SPECIFICITY

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.

Citation

Journal: J.Virol. / Year: 2013
Title: Structural Analysis of the Hemagglutinin from the Recent 2013 H7N9 Influenza Virus.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.

History

Deposition	Jul 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Oct 9, 2024	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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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Validation report

Summary document	4ln8_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ln/4ln8 ftp://data.pdbj.org/pub/pdb/validation_reports/ln/4ln8	HTTPS FTP

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Related structure data

Related structure data	4ln3C 4ln4C 4ln6C 4kth 4kw1 4kwm C: citing same article (ref.)
Similar structure data	4n61-2 4n63-2 4n60-1 6idd-2 4n5j-1 4n5k-1 4lkg-1 4dj8-d 4unx-d 6idd-1 6icx-1 22937 6idz-1 4kon-1 4ln6-1 4ln6-5 4n61-1 5t6s-1 4ln3-5 4n62-1 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) 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

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	#76 - Apr 2006 Hemagglutinin similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #63 - Mar 2005 T-Cell Receptor similarity (5) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Hemagglutinin

B: Hemagglutinin

C: Hemagglutinin

D: Hemagglutinin

E: Hemagglutinin

F: Hemagglutinin

G: Hemagglutinin

H: Hemagglutinin

I: Hemagglutinin

J: Hemagglutinin

K: Hemagglutinin

L: Hemagglutinin

hetero molecules

349 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin

B: Hemagglutinin

C: Hemagglutinin

D: Hemagglutinin

E: Hemagglutinin

F: Hemagglutinin

hetero molecules

defined by author&software
175 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Hemagglutinin

B: Hemagglutinin

hetero molecules

defined by software
58.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Hemagglutinin

D: Hemagglutinin

hetero molecules

defined by software
58.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: Hemagglutinin

F: Hemagglutinin

hetero molecules

defined by software
58.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

G: Hemagglutinin

H: Hemagglutinin

hetero molecules

I: Hemagglutinin

J: Hemagglutinin

K: Hemagglutinin

L: Hemagglutinin

hetero molecules

defined by author&software
174 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

G: Hemagglutinin

H: Hemagglutinin

hetero molecules

defined by software
57.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

I: Hemagglutinin

J: Hemagglutinin

hetero molecules

defined by software
57.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

K: Hemagglutinin

L: Hemagglutinin

hetero molecules

defined by software
57.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	154.361, 154.441, 154.061
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-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	ASP	ASP	GLU	GLU	A	A	1 - 316	5 - 320
2	1	ASP	ASP	GLU	GLU	C	C	1 - 316	5 - 320
1	2	ASP	ASP	GLU	GLU	A	A	1 - 316	5 - 320
2	2	ASP	ASP	GLU	GLU	E	E	1 - 316	5 - 320
1	3	ASP	ASP	GLU	GLU	A	A	1 - 316	5 - 320
2	3	ASP	ASP	GLU	GLU	G	G	1 - 316	5 - 320
1	4	ASP	ASP	GLU	GLU	A	A	1 - 316	5 - 320
2	4	ASP	ASP	GLU	GLU	I	I	1 - 316	5 - 320
1	5	ASP	ASP	GLU	GLU	A	A	1 - 316	5 - 320
2	5	ASP	ASP	GLU	GLU	K	K	1 - 316	5 - 320
1	6	ALA	ALA	ILE	ILE	B	B	5 - 171	5 - 171
2	6	ALA	ALA	ILE	ILE	D	D	5 - 171	5 - 171
1	7	ALA	ALA	ILE	ILE	B	B	5 - 171	5 - 171
2	7	ALA	ALA	ILE	ILE	F	F	5 - 171	5 - 171
1	8	ALA	ALA	ILE	ILE	B	B	5 - 171	5 - 171
2	8	ALA	ALA	ILE	ILE	H	H	5 - 171	5 - 171
1	9	ALA	ALA	ILE	ILE	B	B	5 - 171	5 - 171
2	9	ALA	ALA	ILE	ILE	J	J	5 - 171	5 - 171
1	10	ALA	ALA	ILE	ILE	B	B	5 - 171	5 - 171
2	10	ALA	ALA	ILE	ILE	L	L	5 - 171	5 - 171
1	11	ASP	ASP	GLU	GLU	C	C	1 - 316	5 - 320
2	11	ASP	ASP	GLU	GLU	E	E	1 - 316	5 - 320
1	12	ASP	ASP	GLU	GLU	C	C	1 - 316	5 - 320
2	12	ASP	ASP	GLU	GLU	G	G	1 - 316	5 - 320
1	13	ASP	ASP	GLU	GLU	C	C	1 - 316	5 - 320
2	13	ASP	ASP	GLU	GLU	I	I	1 - 316	5 - 320
1	14	ASP	ASP	GLU	GLU	C	C	1 - 316	5 - 320
2	14	ASP	ASP	GLU	GLU	K	K	1 - 316	5 - 320
1	15	ALA	ALA	ILE	ILE	D	D	5 - 171	5 - 171
2	15	ALA	ALA	ILE	ILE	F	F	5 - 171	5 - 171
1	16	ALA	ALA	ILE	ILE	D	D	5 - 171	5 - 171
2	16	ALA	ALA	ILE	ILE	H	H	5 - 171	5 - 171
1	17	ALA	ALA	ILE	ILE	D	D	5 - 171	5 - 171
2	17	ALA	ALA	ILE	ILE	J	J	5 - 171	5 - 171
1	18	ALA	ALA	ILE	ILE	D	D	5 - 171	5 - 171
2	18	ALA	ALA	ILE	ILE	L	L	5 - 171	5 - 171
1	19	ASP	ASP	GLU	GLU	E	E	1 - 316	5 - 320
2	19	ASP	ASP	GLU	GLU	G	G	1 - 316	5 - 320
1	20	ASP	ASP	GLU	GLU	E	E	1 - 316	5 - 320
2	20	ASP	ASP	GLU	GLU	I	I	1 - 316	5 - 320
1	21	ASP	ASP	GLU	GLU	E	E	1 - 316	5 - 320
2	21	ASP	ASP	GLU	GLU	K	K	1 - 316	5 - 320
1	22	ALA	ALA	ILE	ILE	F	F	5 - 171	5 - 171
2	22	ALA	ALA	ILE	ILE	H	H	5 - 171	5 - 171
1	23	ALA	ALA	ILE	ILE	F	F	5 - 171	5 - 171
2	23	ALA	ALA	ILE	ILE	J	J	5 - 171	5 - 171
1	24	ALA	ALA	ILE	ILE	F	F	5 - 171	5 - 171
2	24	ALA	ALA	ILE	ILE	L	L	5 - 171	5 - 171
1	25	ASP	ASP	GLU	GLU	G	G	1 - 316	5 - 320
2	25	ASP	ASP	GLU	GLU	I	I	1 - 316	5 - 320
1	26	ASP	ASP	GLU	GLU	G	G	1 - 316	5 - 320
2	26	ASP	ASP	GLU	GLU	K	K	1 - 316	5 - 320
1	27	ALA	ALA	ILE	ILE	H	H	5 - 171	5 - 171
2	27	ALA	ALA	ILE	ILE	J	J	5 - 171	5 - 171
1	28	ALA	ALA	ILE	ILE	H	H	5 - 171	5 - 171
2	28	ALA	ALA	ILE	ILE	L	L	5 - 171	5 - 171
1	29	ASP	ASP	GLU	GLU	I	I	1 - 316	5 - 320
2	29	ASP	ASP	GLU	GLU	K	K	1 - 316	5 - 320
1	30	ALA	ALA	ILE	ILE	J	J	5 - 171	5 - 171
2	30	ALA	ALA	ILE	ILE	L	L	5 - 171	5 - 171

NCS ensembles :

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein	Hemagglutinin Mass: 35333.891 Da / Num. of mol.: 6 / Fragment: HA1 subunit residues 19-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21*PLUS
#2: Protein	Hemagglutinin Mass: 20884.959 Da / Num. of mol.: 6 / Fragment: HA2 subunit residues 340-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21*PLUS

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Sugars , 6 types, 21 molecules

#3: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...

Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#4: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}	LINUCS	PDB-CARE

#5: Polysaccharide

beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D- ...

Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGalpb1-3[DNeup5Aca2-6]DGlcpNAcb1-3DGalpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2NCC/3=O][Aad21122h-2a_2-6_5NCC/3=O]/1-2-1-3/a3-b1_b3-c1_b6-d2	WURCS	PDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(6+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#6: Polysaccharide

beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGalpb1-3[DNeup5Aca2-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5NCC/3=O]/1-2-3/a3-b1_a6-c2	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-Galp]{}[(6+2)][a-D-Neup5Ac]{}}	LINUCS	PDB-CARE

#7: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 512.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-6DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2NCC/3=O][Aad21122h-2a_2-6_5NCC/3=O]/1-2/a6-b2	WURCS	PDB2Glycan 1.1.0
[][D-1,3-deoxy-GlcpNAc]{[(6+2)][a-D-Neup5Ac]{}}	LINUCS	PDB-CARE

#9: 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 454 molecules

#8: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.72 Å³/Da / Density % sol: 54.81 %
Crystal grow	Temperature: 293 K / Method: microbatch / pH: 8 Details: 0.2M CaCl2, 20% PEG3350, pH 8.0, Microbatch, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 3, 2013
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 8775 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.5→2.57 Å / % possible all: 89.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→38.62 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.926 / SU B: 22.566 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.558 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24574	6301	5 %	RANDOM
R_work	0.21715	-	-	-
all	0.22	126412	-	-
obs	0.21862	119004	98.19 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 62.627 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	-1.03 Å²	0 Å²
3-	-	-	1.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→38.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22632	0	765	448	23845

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	23879
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	22021
X-RAY DIFFRACTION	r_angle_refined_deg	1.625	1.974	32311
X-RAY DIFFRACTION	r_angle_other_deg	0.925	3.002	50384
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.581	5	2886
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.765	24.536	1164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.358	15	3966
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.84	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	3610
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	27093
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	5571

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.415	428	-
R_work	0.339	7949	-
obs	-	-	89.86 %

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	0.3801	0.3115	0.373	0.826	0.5859	0.5219	-0.0977	0.1338	-0.0632	-0.0035	0.1143	0.0677	-0.0643	0.173	-0.0166	0.0968	-0.0146	0.0485	0.1468	-0.0378	0.0452	-19.2187	-36.5768	31.3035
2	1.3332	0.8739	0.775	0.9577	0.6529	0.5099	0.0769	-0.0678	0.016	0.0217	-0.0456	-0.1071	0.0177	-0.0401	-0.0312	0.0878	-0.0678	0.0001	0.1502	-0.0045	0.0386	3.4987	-5.3041	62.9032
3	0.5307	0.3496	0.6026	0.3327	0.3113	0.8037	-0.0352	-0.0784	0.1268	-0.0581	-0.0706	0.1124	0.0568	-0.0368	0.1057	0.1054	0.0503	-0.0379	0.1384	-0.0152	0.0454	-45.7035	-19.1863	40.5716
4	0.6171	0.8678	0.7813	1.4566	0.9826	1.0646	-0.0584	0.0084	-0.0327	-0.0105	0.1067	-0.068	-0.1279	0.0078	-0.0483	0.0934	-0.0021	0.003	0.1464	-0.055	0.0237	-14.1533	3.5077	71.7676
5	0.8565	0.6147	0.4165	0.5094	0.3867	0.404	0.0975	0.0569	-0.017	0.1415	-0.0242	-0.0412	0.11	-0.0508	-0.0733	0.1045	-0.0294	-0.0173	0.1499	0.0421	0.0238	-36.483	-45.6164	57.9978
6	0.8082	0.5997	0.7271	0.4798	0.6677	1.1686	-0.0334	-0.1191	0.0143	-0.0152	-0.0495	0.0198	-0.0422	-0.0024	0.0829	0.103	0.0077	-0.0531	0.152	-0.0065	0.0375	-5.2801	-14.162	80.5495
7	0.983	0.4592	-0.5207	0.268	-0.2858	0.4017	0.1141	0.0373	-0.0871	0.076	-0.0796	-0.0282	-0.1786	0.0053	-0.0345	0.1304	0.021	0.0664	0.1893	0.0105	0.0592	-3.9428	-59.0668	82.9911
8	0.9354	1.039	-0.7709	1.1842	-0.8686	0.6482	-0.0566	0.0704	0.0141	-0.0048	0.0824	0.0311	0.0395	-0.0953	-0.0258	0.1478	-0.07	0.013	0.1642	0.0361	0.0148	29.3935	-35.6719	52.8063
9	0.2299	-0.2556	-0.3946	0.3844	0.4651	0.8224	-0.0434	-0.0373	-0.0578	-0.0144	-0.0491	0.138	-0.0459	0.0951	0.0925	0.1186	0.0161	-0.0175	0.155	-0.0554	0.0752	-18.1847	-5.8521	-3.9206
10	1.5667	-1.2409	-1.2614	0.9943	1.0176	1.071	0.082	0.0316	0.0123	-0.088	-0.0342	-0.0345	-0.0633	-0.0168	-0.0478	0.1085	0.0423	0.055	0.1573	-0.0096	0.0605	-41.5299	24.2861	29.3394
11	0.4264	-0.5342	-0.2941	0.8931	0.4522	0.311	-0.0517	-0.185	-0.033	-0.0721	0.1043	0.0458	-0.0345	0.0817	-0.0526	0.12	0.0566	0.0165	0.1868	0.0134	0.0713	5.9657	-3.9252	18.1294
12	0.7519	-0.7929	-0.9833	0.8965	1.0303	1.2987	-0.0143	0.0707	-0.088	0.0175	-0.0882	0.0715	0.0202	-0.0416	0.1025	0.0964	0.0214	0.0292	0.2153	-0.0599	0.0463	-24.274	29.4218	41.4694

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 316
2	X-RAY DIFFRACTION	1	A	402 - 411
3	X-RAY DIFFRACTION	2	B	5 - 171
4	X-RAY DIFFRACTION	2	B	500
5	X-RAY DIFFRACTION	3	C	1 - 316
6	X-RAY DIFFRACTION	3	C	402 - 410
7	X-RAY DIFFRACTION	4	D	5 - 171
8	X-RAY DIFFRACTION	4	D	500
9	X-RAY DIFFRACTION	5	E	1 - 316
10	X-RAY DIFFRACTION	5	E	402 - 409
11	X-RAY DIFFRACTION	6	F	5 - 171
12	X-RAY DIFFRACTION	6	F	500
13	X-RAY DIFFRACTION	7	G	1 - 316
14	X-RAY DIFFRACTION	7	G	401 - 407
15	X-RAY DIFFRACTION	8	H	5 - 171
16	X-RAY DIFFRACTION	8	H	500
17	X-RAY DIFFRACTION	9	I	1 - 316
18	X-RAY DIFFRACTION	9	I	401 - 406
19	X-RAY DIFFRACTION	10	J	5 - 171
20	X-RAY DIFFRACTION	10	J	500
21	X-RAY DIFFRACTION	11	K	1 - 316
22	X-RAY DIFFRACTION	11	K	401 - 407
23	X-RAY DIFFRACTION	12	L	5 - 171
24	X-RAY DIFFRACTION	12	L	500

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