PDB-9bt5: The crystal structure of the HA1 domain of hemagglutinin from A/S...

ID or keywords:

Entry

Database: PDB / ID: 9bt5

Title

The crystal structure of the HA1 domain of hemagglutinin from A/Shanghai/02/2013 (H7N9) bound to H7-235 Fab

Components

(Monoclonal antibody H7-235 ...) x 2
Hemagglutinin

Keywords

IMMUNE SYSTEM / antibody / influenza / hemagglutinin

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

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Buchman, C.D. / Dong, J. / Crowe, J.E.

Funding support

United States, 1items

Citation

Journal: JCI Insight / Year: 2025
Title: Pan-H7 influenza human antibody virus neutralization depends on avidity and steric hindrance.
Authors: Gilchuk, I.M. / Dong, J. / Irving, R.P. / Buchman, C.D. / Armstrong, E. / Turner, H.L. / Li, S. / Ward, A.B. / Carnahan, R.H. / Crowe Jr., J.E.

History

Deposition	May 14, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9bt5.cif.gz	613.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9bt5.ent.gz	420.4 KB	Display	PDB format
PDBx/mmJSON format	9bt5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/9bt5 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/9bt5	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #76 - Apr 2006 Hemagglutinin similarity (6) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #113 - May 2009 Influenza Neuraminidase similarity (1) #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)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#76 - Apr 2006
Hemagglutinin
similarity (6)
#170 - Feb 2014
Broadly Neutralizing Antibodies
similarity (5)
#113 - May 2009
Influenza Neuraminidase
similarity (1)
#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

C: Monoclonal antibody H7-235 heavy chain

D: Monoclonal antibody H7-235 light chain

B: Hemagglutinin

E: Monoclonal antibody H7-235 heavy chain

F: Monoclonal antibody H7-235 light chain

hetero molecules

146 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin

C: Monoclonal antibody H7-235 heavy chain

D: Monoclonal antibody H7-235 light chain

hetero molecules

defined by author
72.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hemagglutinin

E: Monoclonal antibody H7-235 heavy chain

F: Monoclonal antibody H7-235 light chain

hetero molecules

defined by author
72.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	240.603, 95.053, 99.265
Angle α, β, γ (deg.)	90.000, 95.850, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	B-1122- HOH

-
Antibody , 2 types, 4 molecules CEDF

#2: Antibody	Monoclonal antibody H7-235 heavy chain Mass: 24698.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody	Monoclonal antibody H7-235 light chain Mass: 23975.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Protein / Non-polymers , 2 types, 176 molecules AB

#1: Protein	Hemagglutinin Mass: 23716.711 Da / Num. of mol.: 2 / Fragment: HA1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Shanghai/02/2013(H7N9)) Gene: HA / Production host: Homo sapiens (human) / References: UniProt: R4NN21
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

-
Sugars , 2 types, 4 molecules

#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.: 2 / Source method: obtained synthetically / 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

#5: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.9 Å³/Da / Density % sol: 68.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M sodium chloride, 8-10% PEG 6000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 29, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.5→49.37 Å / Num. obs: 76766 / % possible obs: 99.6 % / Redundancy: 3.9 % / B_iso Wilson estimate: 46.63 Å² / R_merge(I) obs: 0.096 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.862 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11112 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→49.37 Å / SU ML: 0.3749 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.251	3959	5.16 %
R_work	0.195	72739	-
obs	0.1979	76698	99.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 61.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→49.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9851	0	70	174	10095

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0099	10152
X-RAY DIFFRACTION	f_angle_d	1.1128	13817
X-RAY DIFFRACTION	f_chiral_restr	0.0589	1537
X-RAY DIFFRACTION	f_plane_restr	0.009	1795
X-RAY DIFFRACTION	f_dihedral_angle_d	6.623	1421

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.53	0.474	150	0.3847	2532	X-RAY DIFFRACTION	98.82
2.53-2.56	0.4285	155	0.3558	2527	X-RAY DIFFRACTION	98.78
2.56-2.6	0.3827	136	0.3181	2606	X-RAY DIFFRACTION	99.1
2.6-2.63	0.3656	144	0.2954	2568	X-RAY DIFFRACTION	99.01
2.63-2.67	0.3573	142	0.2971	2567	X-RAY DIFFRACTION	98.8
2.67-2.71	0.3159	139	0.2817	2574	X-RAY DIFFRACTION	99.16
2.71-2.75	0.3756	136	0.2725	2611	X-RAY DIFFRACTION	99.1
2.75-2.8	0.3174	127	0.2691	2569	X-RAY DIFFRACTION	99.08
2.8-2.84	0.307	145	0.2641	2547	X-RAY DIFFRACTION	99.12
2.84-2.9	0.3376	151	0.2697	2596	X-RAY DIFFRACTION	99.28
2.9-2.95	0.3338	151	0.2761	2544	X-RAY DIFFRACTION	99.3
2.95-3.01	0.3844	129	0.2538	2636	X-RAY DIFFRACTION	99.46
3.01-3.08	0.3116	143	0.2534	2572	X-RAY DIFFRACTION	99.38
3.08-3.15	0.3356	137	0.2355	2595	X-RAY DIFFRACTION	99.53
3.15-3.23	0.292	147	0.2213	2597	X-RAY DIFFRACTION	99.53
3.23-3.32	0.266	138	0.2121	2592	X-RAY DIFFRACTION	99.56
3.32-3.41	0.2635	146	0.202	2586	X-RAY DIFFRACTION	99.56
3.41-3.52	0.2588	135	0.2019	2632	X-RAY DIFFRACTION	99.5
3.52-3.65	0.2376	134	0.1903	2600	X-RAY DIFFRACTION	99.64
3.65-3.8	0.2111	117	0.1779	2653	X-RAY DIFFRACTION	99.64
3.8-3.97	0.2216	132	0.1624	2605	X-RAY DIFFRACTION	99.74
3.97-4.18	0.225	127	0.1544	2618	X-RAY DIFFRACTION	99.71
4.18-4.44	0.1961	147	0.1358	2612	X-RAY DIFFRACTION	99.75
4.44-4.78	0.1832	134	0.1312	2620	X-RAY DIFFRACTION	99.78
4.78-5.26	0.1767	171	0.1361	2603	X-RAY DIFFRACTION	99.86
5.26-6.02	0.1752	139	0.1496	2630	X-RAY DIFFRACTION	99.89
6.02-7.58	0.2267	160	0.1715	2642	X-RAY DIFFRACTION	99.96
7.58-49.37	0.2127	147	0.1783	2705	X-RAY DIFFRACTION	99.65

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	0.813874794153	-0.107817975206	0.0164372200249	0.017607152171	5.53551786909E-5	-0.00492156068346	-0.117711637058	-0.686877193934	0.150724640037	0.0127388530799	0.0860437096377	-0.0122265728592	0.377148089858	0.589524522128	-0.00975856932937	0.541142148817	0.100440684732	-0.0295365573709	0.834701639201	0.125298591564	0.339902502839	5.18919392945	29.8613669839	34.4509171078
2	0.0728540067211	-0.0947340418919	-0.271624891139	0.12601847028	0.24687555814	0.642051041869	-0.0190119878436	-0.398913376372	-0.0881190476592	0.0340545607525	-0.0694657217986	0.1067473788	0.0376226736155	0.201961876419	-0.000202355301398	0.422902362011	0.0401655409117	0.0126029212139	0.68095035816	0.103459394294	0.308656221539	2.41492056589	31.5407192768	34.6877977807
3	0.18928254421	0.0915025713857	0.0745309795327	0.22184427071	0.00551594134019	0.0331017711692	0.056204888554	-0.390271059115	-0.271201301915	0.0627950523816	0.173178985434	-0.0440372966925	0.298400453486	0.0592907937719	7.224888579E-5	0.674780138703	-0.00108767311048	0.0547043113981	0.668449225051	0.101005086347	0.522123110233	-3.50123441141	26.9156699675	29.4488919587
4	0.297608821042	0.018813771576	-0.0870976273834	-0.00493109674835	-0.0330211476479	0.0401966043242	0.106383998887	-0.443165569915	0.00149997758022	-0.0762661326405	-0.186959476375	0.0882566165842	-0.0773976487258	-0.056418497924	7.4601116502E-5	0.319411819028	-0.0454761210517	-0.00169993619306	0.510917874217	-0.0222847142345	0.3397246473	7.47164735382	45.4014712403	21.2767152591
5	0.0734050857498	-0.0369678849598	0.00072701451354	0.0183789655462	0.00592196055524	0.0360349583247	-0.137892521888	-0.713274457961	-0.173446696112	-0.0262848950036	0.147264637234	-0.188631330665	-0.0180206214428	0.73965642255	0.00101305625326	0.434009866709	-0.0321984608041	-0.0489857568843	0.749465785473	0.00162785729225	0.350332505307	6.49144367231	42.8089918054	25.5230607051
6	0.333165693614	0.191440421228	-0.377420163768	0.343676248844	-0.288176721875	0.437664586892	0.00849396200785	-0.214782238976	0.0652555772935	0.142038375544	0.0434362019611	0.147165621628	-0.068831778612	0.0648191717125	-0.000117765327817	0.378473173048	0.021427227801	0.0235109613808	0.314200264392	-0.029140839592	0.354117697727	-2.26462255296	46.8282383559	19.4605801991
7	0.458674054335	-0.23449622777	-0.154323086577	0.121507487564	0.114490255673	0.149330398349	0.233377134248	-0.261342645329	-0.117924877228	-0.267345243326	-0.25590672042	-0.345146872068	-0.0855701723567	-0.279160221329	0.000518458765656	0.386724178876	0.0543304820368	-0.000305853040041	0.396720501614	-0.0333069801915	0.46444168762	-12.8301796742	45.4083992065	19.2221014215
8	0.0972073089765	0.0668665881888	-0.119483271913	0.0190777346089	0.0109676675674	0.14237017972	0.0741510352194	-0.415002583386	0.0440529786397	0.554611993069	-0.295696498201	0.166765131691	0.327858835796	-0.0576434620629	3.23318450319E-5	0.506966566328	-0.0494850629148	0.000182102009081	0.558748815894	-0.0498536208737	0.390832294628	-4.62523799708	46.3361078706	31.5757330517
9	0.220798779503	0.0224902270659	-0.0973400862486	0.056874055388	0.119773424684	0.241704213196	-0.101638037349	0.10404496775	-0.163903327414	0.133679447914	0.0493324587408	-0.279524284404	0.0731809353241	-0.385164986139	0.000144889205322	0.410365092696	0.0711300847017	-0.0073937706144	0.508676755798	-0.0919044712444	0.416223226052	-6.16516497629	39.4962982273	16.2814196714
10	0.00966224955632	-0.0319671701485	-0.0306468880846	0.145664770353	0.0452651542156	0.0402273324612	-0.343090097235	-0.819916859168	-0.0963478541754	0.544277385682	0.130272616847	-0.116462392691	-0.0216678274367	-0.145939295812	0.000188127221482	0.711286984032	0.0580843569241	0.0252135849248	0.754548970086	0.0379793315203	0.534594634953	0.248152330791	23.6315121504	30.7155745548
11	1.23329902416	0.234307695798	-0.0205270143727	1.01381625835	0.223363195793	0.314161738887	-0.117686371733	-0.393701466146	-0.11135342646	0.00452411384193	0.109910479083	-0.0918458615842	0.0811962540919	0.125945707787	-1.95346585945E-5	0.323467681232	0.069620257133	-0.030172820188	0.497500863553	0.050892509233	0.382289174907	27.0824877088	36.0294450729	15.1225603672
12	0.94307430768	-0.021152019059	0.627950954699	0.675542635988	-0.123848393242	0.52852392017	-0.382707581219	0.573658594443	0.10434783467	0.077427562751	0.225201343012	0.131904735476	-0.249860881398	0.833253198636	0.00951202038046	0.530456580338	-0.250401548284	-0.0583294586856	0.53693750229	0.135317550647	0.451585448291	50.0972553278	63.639812056	12.3896344615
13	1.11855042106	-0.257721169475	-0.142212310635	0.696822825733	-0.919526746402	1.40128486963	-0.0358710891214	0.29104246118	-0.0242910930616	-0.0995564179624	-0.00462677390118	-0.0321028821983	-0.0813424758201	-0.0288499995112	-1.82079407065E-5	0.307554795121	-0.0152011515315	-0.0216131089138	0.414988399765	0.0273682510959	0.327246298101	18.3315222226	49.7112260362	0.334331563438
14	0.392056342004	-0.213647613198	-0.0283983251736	1.11291283801	-0.0891712918434	0.865808408291	-0.432689495429	1.29210859148	0.235736698657	-0.130934779029	0.0284552573084	-0.168006965533	-0.326687142241	0.938215475788	-0.00445842014354	0.675593178606	-0.317638214865	0.00812285386493	1.38342016983	0.250654368652	0.720214448989	50.1694768946	64.7433122815	-4.0673932496
15	0.0781989802051	-0.0676226146979	0.108657765811	0.0255596259522	-0.069401293103	0.114748157754	-0.22026047821	0.381484042558	-0.0620021047506	-0.0794501487263	0.32278356986	0.0161638418381	-0.0281327931784	0.197394471422	-0.000299367364558	0.460647048372	-0.0647812176086	-0.032807683609	0.652330248676	0.056652535594	0.444681080155	11.9737320219	52.4642118298	52.6240393169
16	0.531822612618	0.177698211839	-0.342328118814	0.532267090931	-0.593865119643	0.438079651513	-0.144504301585	0.440480063398	0.00307503177072	0.00300654888914	0.09050353566	0.0603844676629	0.142316780627	-0.447798668916	-2.13795769968E-5	0.419580246017	-0.0599606975855	-0.00402768126361	0.591788886865	-0.0382847441935	0.378932163694	15.049722648	45.9102508133	57.8685136492
17	1.34457623464	-0.234237389198	-0.860475976028	0.659650201039	-0.381037774132	0.865213286058	-0.102334836602	0.0294573012474	-0.150352776758	0.111895625576	-0.0129614086777	-0.041520376855	0.232052801031	-0.413477036114	-8.34502905095E-5	0.388059228771	-0.0575708350785	0.00422610754644	0.316121379442	-0.0682108475928	0.330949600896	17.7438255943	35.6062151386	66.9753011973
18	0.0565227039478	-0.0388874266809	0.0869340087241	0.0820215902037	0.0520571728283	0.149472621978	-0.0703674815683	0.0364819268199	0.0664999873745	-0.229527354636	0.208762260782	-0.0801039540143	-0.0535564845423	-0.495979662924	-0.000479610112143	0.545332834666	0.0560405940843	-0.0749916998263	0.56067335036	0.0476274385373	0.433224629485	8.67248626389	57.1549208921	59.3393530983
19	0.19107583825	-0.0834602049803	-0.268856275434	0.426985729624	0.444256666301	0.48217558132	-0.0177511588292	0.409422632987	0.0650937651035	-0.0377403477484	0.00486813230092	0.119892207786	-0.182632697933	-0.614431064644	0.000235108617796	0.3783571316	-0.0693010992151	0.00273959993472	0.364160681821	0.0257612881684	0.364658429594	36.6074938618	50.3371860232	41.8980919712
20	0.234189342479	0.301260084876	-0.56367571617	0.718325341099	-0.194173764037	1.32997775017	-0.0794255697271	-0.168489577188	0.0215892602067	-0.0821329645736	0.0874895870706	-0.0180451253889	0.0210922387973	-0.117420894023	-2.801491507E-5	0.356373082094	-0.0122330786429	0.00449362210973	0.2444116971	-0.00121912514855	0.389586246498	40.5122142235	54.9236941904	49.8619637073
21	0.693313619599	-0.208237280902	0.242285462069	0.257547211384	-0.662700733306	0.832659032327	0.205060290834	0.48885711555	-0.0342743412426	0.0621177096972	-0.301222758639	0.0115795602113	0.0723500608734	0.354591578104	-1.77235621982E-5	0.394117386408	-0.00485518442904	-0.0408354249639	0.515545142589	-0.0427604215431	0.358698983848	61.1132186204	37.8710533024	32.6937223395
22	0.396555765574	-0.597347473866	0.247229071442	0.745192372108	-0.639373526599	0.509596409453	0.260303926428	0.386386477811	-0.10657463143	0.0336464296976	-0.0312331503193	0.276860044667	0.0722255529377	0.435229394463	0.00047272135859	0.38248967324	0.105207031	-0.0665466910408	0.460153195052	-0.118404297225	0.494031455754	61.6602971065	32.0430126078	27.7909372303
23	1.33553414264	-0.113772473527	0.430453108045	1.02805046756	-0.255603346325	0.713860247306	-0.0746312696451	-0.148787123783	0.0183971263533	0.0401717698167	0.0260942813826	-0.117958827932	0.0559517048542	0.172601117387	-6.38681781613E-5	0.366541710777	0.0167896379029	0.034817580813	0.272270231439	0.000884553530669	0.397985465086	47.4188398263	40.4607528146	62.6694613997
24	1.33125558779	-0.752296293443	0.420218492656	0.46438681389	-0.0234287822615	1.05353460916	-0.0369406469789	0.250697055962	0.0393284371674	0.107303961412	-0.136373266338	-0.0380159610283	-0.0139219112	0.68960223524	0.0013276245439	0.268336572233	-0.0379447473549	-0.00595959349884	0.341509340095	0.0306729113792	0.384973483118	67.5180536499	36.2158563613	45.5098361936

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 46 through 66 )	A	A	46 - 66	1 - 21
2	2	chain 'A' and (resid 67 through 94 )	A	A	67 - 94	22 - 49
3	3	chain 'A' and (resid 95 through 112 )	A	A	95 - 112	50 - 67
4	4	chain 'A' and (resid 113 through 132 )	A	A	113 - 132	68 - 87
5	5	chain 'A' and (resid 133 through 142 )	A	A	133 - 142	88 - 97
6	6	chain 'A' and (resid 143 through 186 )	A	A	143 - 186	98 - 141
7	7	chain 'A' and (resid 187 through 204 )	A	A	187 - 204	142 - 159
8	8	chain 'A' and (resid 205 through 228 )	A	A	205 - 228	160 - 183
9	9	chain 'A' and (resid 229 through 246 )	A	A	229 - 246	184 - 201
10	10	chain 'A' and (resid 247 through 262 )	A	A	247 - 262	202 - 217
11	11	chain 'C' and (resid 1 through 123 )	C	D	1 - 123	1 - 123
12	12	chain 'C' and (resid 124 through 223 )	C	D	124 - 223	124 - 217
13	13	chain 'D' and (resid 1 through 118 )	D	E	1 - 118	1 - 118
14	14	chain 'D' and (resid 119 through 216 )	D	E	119 - 216	119 - 216
15	15	chain 'B' and (resid 46 through 69 )	B	F	46 - 69	1 - 24
16	16	chain 'B' and (resid 70 through 142 )	B	F	70 - 142	25 - 97
17	17	chain 'B' and (resid 143 through 246 )	B	F	143 - 246	98 - 201
18	18	chain 'B' and (resid 247 through 262 )	B	F	247 - 262	202 - 217
19	19	chain 'E' and (resid 1 through 33 )	E	I	1 - 33	1 - 33
20	20	chain 'E' and (resid 34 through 111 )	E	I	34 - 111	34 - 111
21	21	chain 'E' and (resid 112 through 157 )	E	I	112 - 157	112 - 157
22	22	chain 'E' and (resid 158 through 223 )	E	I	158 - 223	158 - 223
23	23	chain 'F' and (resid 1 through 66 )	F	J	1 - 66	1 - 66
24	24	chain 'F' and (resid 67 through 216 )	F	J	67 - 216	67 - 216

-
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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 4 molecules CEDF

-
Protein / Non-polymers , 2 types, 176 molecules AB

-
Sugars , 2 types, 4 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Antibody , 2 types, 4 molecules CEDF

-Protein / Non-polymers , 2 types, 176 molecules AB

-Sugars , 2 types, 4 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 4 molecules CEDF

-
Protein / Non-polymers , 2 types, 176 molecules AB

-
Sugars , 2 types, 4 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi