PDB-9i42: Structure of anti-EV71 human monoclonal antibody 16-2-2D Fab

ID or keywords:

Entry

Database: PDB / ID: 9i42

Title

Structure of anti-EV71 human monoclonal antibody 16-2-2D Fab

Components

heavy chain 1
light chain 1

Keywords

ANTIVIRAL PROTEIN / EV71 / antibody / 16-2-2D / Fab

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Zhou, D. / Ren, J. / Stuart, D.I.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: Fine antigenic mapping of human enterovirus 71 from structures of cognate complexes for a panel of 12 patient derived monoclonal antibodies
Authors: Zhou, D. / Ren, J. / Stuart, D.I.

History

Deposition	Jan 24, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i42.cif.gz	432.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9i42.ent.gz	293.7 KB	Display	PDB format
PDBx/mmJSON format	9i42.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i4/9i42 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/9i42	HTTPS FTP

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Related structure data

Related structure data	9i3wC 9i3xC 9i3zC 9i40C 9i41C 9i43C 9i45C 9i4bC 9i4cC 9i4dC 9i4eC C: citing same article (ref.)

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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)

Deposited unit

L: light chain 1

H: heavy chain 1

A: light chain 1

B: heavy chain 1

hetero molecules

100 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: light chain 1

H: heavy chain 1

hetero molecules

defined by author
Evidence: gel filtration
50.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: light chain 1

B: heavy chain 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.290, 104.010, 86.090
Angle α, β, γ (deg.)	90.000, 103.990, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 22 or resid 24...
d_2	ens_1	(chain "L" and (resid 2 through 22 or resid 24...
d_1	ens_2	(chain "B" and (resid 2 through 50 or resid 52...
d_2	ens_2	(chain "H" and (resid 2 through 50 or resid 52...

NCS domain segments:

Dom-ID	Component-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
d_1	1	ens_1	SER	SER	CYS	CYS	A	C	2 - 22	2 - 22
d_1	2	ens_1	GLY	GLY	GLN	GLN	A	C	24 - 54	24 - 54
d_1	3	ens_1	PRO	PRO	ASP	ASP	A	C	56 - 94	56 - 94
d_1	4	ens_1	LEU	LEU	TYR	TYR	A	C	96 - 99	96 - 99
d_1	5	ens_1	PHE	PHE	TRP	TRP	A	C	101 - 152	101 - 152
d_1	6	ens_1	ALA	ALA	SER	SER	A	C	154 - 169	154 - 169
d_1	7	ens_1	GLN	GLN	HIS	HIS	A	C	171 - 192	171 - 192
d_1	8	ens_1	SER	SER	THR	THR	A	C	194 - 213	194 - 213
d_2	1	ens_1	SER	SER	CYS	CYS	L	A	2 - 22	2 - 22
d_2	2	ens_1	GLY	GLY	GLN	GLN	L	A	24 - 54	24 - 54
d_2	3	ens_1	PRO	PRO	ASP	ASP	L	A	56 - 94	56 - 94
d_2	4	ens_1	LEU	LEU	TYR	TYR	L	A	96 - 99	96 - 99
d_2	5	ens_1	PHE	PHE	TRP	TRP	L	A	101 - 152	101 - 152
d_2	6	ens_1	ALA	ALA	SER	SER	L	A	154 - 169	154 - 169
d_2	7	ens_1	GLN	GLN	HIS	HIS	L	A	171 - 192	171 - 192
d_2	8	ens_1	SER	SER	THR	THR	L	A	194 - 213	194 - 213
d_1	1	ens_2	VAL	VAL	MET	MET	B	D	2 - 50	2 - 50
d_1	2	ens_2	ARG	ARG	GLY	GLY	B	D	52 - 56	52 - 56
d_1	3	ens_2	THR	THR	LEU	LEU	B	D	58 - 86	58 - 86
d_1	4	ens_2	PRO	PRO	SER	SER	B	D	88 - 147	88 - 147
d_1	5	ens_2	GLY	GLY	GLY	GLY	B	D	153 - 158	153 - 158
d_1	6	ens_2	LEU	LEU	SER	SER	B	D	160 - 199	160 - 199
d_1	7	ens_2	VAL	VAL	ILE	ILE	B	D	201 - 214	201 - 214
d_1	8	ens_2	ASN	ASN	LYS	LYS	B	D	216 - 233	216 - 233
d_2	1	ens_2	VAL	VAL	MET	MET	H	B	2 - 50	2 - 50
d_2	2	ens_2	ARG	ARG	GLY	GLY	H	B	52 - 56	52 - 56
d_2	3	ens_2	THR	THR	LEU	LEU	H	B	58 - 86	58 - 86
d_2	4	ens_2	PRO	PRO	SER	SER	H	B	88 - 147	88 - 147
d_2	5	ens_2	GLY	GLY	GLY	GLY	H	B	153 - 158	153 - 158
d_2	6	ens_2	LEU	LEU	SER	SER	H	B	160 - 199	160 - 199
d_2	7	ens_2	VAL	VAL	ILE	ILE	H	B	201 - 214	201 - 214
d_2	8	ens_2	ASN	ASN	LYS	LYS	H	B	216 - 233	216 - 233

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.810300230285, -0.040769812315, -0.584595038641), (0.000829177394851, -0.997496218809, 0.070714962542), (-0.586014376329, -0.0577850834236, -0.808237610403)	33.3793986083, -17.7000237783, 26.5739568302
2	given	(0.780429007075, 0.0116951070118, -0.625135016926), (0.0577372562999, -0.996901020198, 0.0534300024629), (-0.622572866539, -0.0777919044645, -0.778685716737)	34.6245063146, -16.7362738099, 23.6930933485

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody	light chain 1 Mass: 22908.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody	heavy chain 1 Mass: 26497.717 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 439 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.79 Å³/Da / Density % sol: 55.86 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 0.05 M ammonium sulphate, 0.1 M bis-Tris, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.92→44.15 Å / Num. obs: 82492 / % possible obs: 100 % / Redundancy: 43.2 % / B_iso Wilson estimate: 38.51 Å² / CC_1/2: 1 / Net I/σ(I): 20.4
Reflection shell	Resolution: 1.92→1.94 Å / Num. unique obs: 4093 / CC_1/2: 0.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.92→44.15 Å / SU ML: 0.2241 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1918	4018	4.88 %
R_work	0.164	78345	-
obs	0.1654	82363	99.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→44.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6697	0	98	419	7214

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	6982
X-RAY DIFFRACTION	f_angle_d	0.986	9512
X-RAY DIFFRACTION	f_chiral_restr	0.0649	1051
X-RAY DIFFRACTION	f_plane_restr	0.0079	1213
X-RAY DIFFRACTION	f_dihedral_angle_d	13.2426	2496

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	C	A	X-RAY DIFFRACTION	Torsion NCS	1.43169216733
ens_2	d_2	D	B	X-RAY DIFFRACTION	Torsion NCS	1.36735411291

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 (%)
1.92-1.94	0.3544	147	0.3634	2616	X-RAY DIFFRACTION	98.78
1.94-1.97	0.2999	137	0.2769	2702	X-RAY DIFFRACTION	99.47
1.97-1.99	0.2536	132	0.249	2702	X-RAY DIFFRACTION	99.82
1.99-2.02	0.2737	136	0.2164	2650	X-RAY DIFFRACTION	99.86
2.02-2.04	0.248	154	0.2043	2729	X-RAY DIFFRACTION	99.9
2.05-2.07	0.2376	132	0.1991	2671	X-RAY DIFFRACTION	99.96
2.07-2.11	0.244	127	0.1968	2732	X-RAY DIFFRACTION	99.79
2.11-2.14	0.2106	147	0.1901	2655	X-RAY DIFFRACTION	100
2.14-2.17	0.2149	128	0.1955	2707	X-RAY DIFFRACTION	99.82
2.17-2.21	0.2475	145	0.1869	2716	X-RAY DIFFRACTION	99.97
2.21-2.25	0.2364	152	0.1786	2673	X-RAY DIFFRACTION	99.96
2.25-2.29	0.2681	128	0.1922	2675	X-RAY DIFFRACTION	99.86
2.29-2.34	0.2409	132	0.1829	2726	X-RAY DIFFRACTION	99.97
2.34-2.39	0.244	144	0.1809	2669	X-RAY DIFFRACTION	99.96
2.39-2.45	0.244	151	0.1836	2705	X-RAY DIFFRACTION	99.93
2.45-2.51	0.2217	141	0.1717	2678	X-RAY DIFFRACTION	100
2.51-2.58	0.2434	135	0.1709	2695	X-RAY DIFFRACTION	99.93
2.58-2.65	0.2061	158	0.1742	2722	X-RAY DIFFRACTION	99.97
2.65-2.74	0.2683	138	0.1785	2677	X-RAY DIFFRACTION	100
2.74-2.84	0.2169	134	0.1755	2700	X-RAY DIFFRACTION	99.89
2.84-2.95	0.2026	144	0.1784	2695	X-RAY DIFFRACTION	100
2.95-3.08	0.2039	124	0.1713	2728	X-RAY DIFFRACTION	99.96
3.08-3.25	0.1865	136	0.1601	2710	X-RAY DIFFRACTION	100
3.25-3.45	0.1882	125	0.1617	2721	X-RAY DIFFRACTION	100
3.45-3.71	0.1752	142	0.16	2737	X-RAY DIFFRACTION	100
3.72-4.09	0.1629	131	0.1403	2716	X-RAY DIFFRACTION	100
4.09-4.68	0.1317	159	0.1255	2710	X-RAY DIFFRACTION	99.97
4.68-5.89	0.1461	142	0.1356	2728	X-RAY DIFFRACTION	100
5.89-44.15	0.1969	117	0.1688	2800	X-RAY DIFFRACTION	99.86

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	0.549085712486	-1.08707790073	-0.187729884084	5.32030264997	-1.50413541797	3.88265078806	0.120147810648	0.200205405772	0.179896963894	0.125258784413	-0.215676781197	-0.172349175732	-0.145980734088	0.132391811344	0.116039887129	0.382822151972	-0.0547112568289	0.0155022381787	0.388537921644	0.0386066254099	0.308692080749	-1.48544203741	-9.88021883648	22.3780676733
2	2.36427829211	-1.76006159115	-1.10709011907	4.72044850763	-0.817184341682	2.15690029889	0.291222301318	0.0638972206117	0.397436646796	0.347763588681	-0.210306929581	-0.327948780409	-0.407338579196	0.209679266471	-0.085207303476	0.515725334231	-0.0841036791868	0.0393389003891	0.429629462305	0.0141887646565	0.320104689253	0.687656910168	-5.71494163524	27.6314290541
3	1.71533738232	-1.32762008845	-0.56172151083	3.02312388318	0.879650372616	0.45518683987	0.243346698828	-0.12912025363	0.241330972658	0.106650319653	-0.163475696022	-0.341550463423	-0.211908006542	0.0791732404706	-0.0561644900116	0.527304359326	-0.0394531012896	0.0498890379777	0.47537934763	0.0277743082539	0.323256868816	-0.810049069289	-8.91922984201	33.0768856853
4	3.55206779635	-0.5523408747	0.211048021921	3.77044951151	1.00350433309	4.05108704698	-0.178482550659	-0.186013902022	-0.572422692651	0.086954926385	-0.0360255231947	0.0940377590184	0.503077472619	-0.0612681976105	0.214342421535	0.467317762715	0.0444694352729	0.125806562621	0.330167827643	-0.00531773858606	0.382141872413	-19.9559753042	3.31150508081	50.0128432706
5	4.23764195638	-0.520317671244	0.0055089793042	4.72740059645	0.117058182517	7.93093322257	-0.309025827191	-0.750082939299	-0.265450638558	0.498976129738	0.249633093119	-0.295202117745	0.470512433188	0.489594531301	0.0856953206535	0.522196449613	0.18549273734	0.0886766409772	0.449369132118	0.0194011912078	0.415610967039	-15.7672041133	5.70894950437	55.0590400024
6	4.38309513405	-0.446404262178	-0.69268495294	2.84766050321	0.160083013832	0.651814915695	0.0446069857647	-0.0765095889794	-0.0608523092826	0.128976858528	-0.0346434331386	0.0730064418444	-0.0225377924977	-0.0382784789601	-0.01301487068	0.29927441022	-0.0015436216146	-0.00280974062692	0.337202504789	0.00760910749812	0.228580255582	7.51676697829	9.81862297711	7.44377577507
7	1.00829183077	0.927290788111	0.126786621046	1.9380721185	0.718957828822	-0.033554097046	0.0268352700796	0.0024559199868	0.236023149326	-0.0255220517512	-0.176218246622	0.523417136855	-0.000790672140046	-0.0210334584293	0.151497290927	0.338045374879	0.018936448117	-0.0180025247016	0.375703738504	0.00542770410348	0.366361478886	-18.8675628366	-11.6323697038	2.1082504365
8	2.08046803708	0.910825936191	0.014900642263	7.50779510476	-0.132220151295	1.66481701838	-0.203525081122	-0.0996630255948	0.0935722211203	0.158116813697	0.0618046979607	0.345159209395	-0.0377848049754	-0.186858227921	0.134781031016	0.303897436042	0.0307672535841	1.38341297783E-5	0.375327303034	-0.062946532927	0.363466295527	-24.6756752583	-13.9689320232	5.98556252922
9	3.51029980588	0.833465193741	-1.18671490896	3.88017932831	-0.648861975623	1.31451739316	0.00870541000012	0.158889274601	-0.0797878844306	-0.148258001573	-0.04443419032	-0.185701237405	0.0783497685459	0.00715100333884	0.0427932331014	0.277193740539	0.0286011584162	-0.0196094760546	0.327842859986	0.00558442947877	0.256493055985	16.8259762083	-8.4105313952	1.87245628498
10	2.53091992149	2.03478977784	-1.11935624414	4.60130666315	-1.26419735422	0.569658641856	-0.0170734517942	0.0409596613285	-0.164103852209	-0.214011964888	-0.0851917336528	-0.476083869984	0.0451000735773	0.173583222463	0.0863631090013	0.298713496661	0.0399015457146	0.00334493263496	0.364597733543	0.00464229066462	0.302796299267	16.4222291904	-8.16505260539	1.71140310143
11	2.9960827718	-0.392783780755	0.522709838872	2.84093555636	-0.177592386592	4.23069821367	-0.0206635800099	0.323522028561	0.193023810109	-0.325825087839	-0.0163398759009	0.114030967219	-0.222044374447	-0.270812662817	0.0252518182265	0.313618794273	-0.00318550506804	0.00551626684621	0.329646485849	0.0184293587932	0.340457558841	-13.1665511349	-19.767377849	-6.75978460054
12	2.70271349364	0.0789839539461	-1.05985228816	4.02135752571	0.0758501109461	2.22919932423	0.00893840056802	-0.0346279144084	-0.0445918892356	0.337143011287	0.066143750063	0.393927927462	0.0129172468322	-0.175035295346	-0.0834601339741	0.381871437839	-0.0564783538395	0.0730717758492	0.353790513672	0.0372436108072	0.307893494462	-9.30338179967	-26.8451746334	33.5549857622
13	0.369263431247	-1.39773786808	-0.453553270813	2.5948045906	1.86469406687	0.922512162836	-0.242817371487	-0.0621808839012	-0.191735826588	0.520158685607	0.0269815821764	0.553080971983	0.267335446089	-0.0236503339657	0.2421276325	0.530836602655	-0.0256966400619	0.145230974757	0.436917399727	0.0140991867911	0.491828851195	-19.9244880278	-10.9078376533	42.0263430867
14	2.26968030578	0.402068511076	-0.489185752435	5.82911148849	-0.806197527571	2.65903948103	-0.28633607222	-0.0433402415135	-0.590615810413	0.0632129126588	-0.0883808928182	1.26541926016	0.559703556599	-0.383014284969	0.387547851907	0.532039192215	-0.0808165369618	0.181194952375	0.461877960374	-0.0923123941422	0.77490908442	-36.0785375658	-0.192519561792	50.2209832983
15	4.55595695675	-2.70496733151	1.255575911	7.28840515161	-2.17252701075	5.37288848217	-0.2375390008	-0.447345669342	0.476832073197	1.0454284254	0.144987426288	-0.341798200631	-1.27161006808	0.00342932319552	0.157091897571	0.634835934757	-0.116195290375	0.107360990992	0.400900894634	-0.0178552945926	0.303896961989	-3.87731210062	1.0639252281	33.1960212387
16	1.88024275641	-1.38654083178	-1.23278245886	4.34725478948	-0.708669664292	2.67044846419	-0.0418700152583	-0.403651365828	0.287628395192	0.742804975877	-0.0536070994953	-0.45203952224	-0.454565908316	0.43243643782	0.0647570588485	0.474732859149	-0.123954826466	-0.00871004851109	0.421564849579	0.00268763581556	0.299524836729	3.94119658707	-7.49676941773	31.8118975258

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 'B' and (resid 41 through 67 )	B	D	41 - 67	41 - 67
2	2	chain 'B' and (resid 68 through 107 )	B	D	68 - 107	68 - 107
3	3	chain 'B' and (resid 108 through 138 )	B	D	108 - 138	108 - 138
4	4	chain 'B' and (resid 139 through 194 )	B	D	139 - 194	139 - 190
5	5	chain 'B' and (resid 195 through 233 )	B	D	195 - 233	191 - 229
6	6	chain 'L' and (resid 1 through 104 )	L	A	1 - 104	1 - 104
7	7	chain 'L' and (resid 105 through 133 )	L	A	105 - 133	105 - 133
8	8	chain 'L' and (resid 134 through 214 )	L	A	134 - 214	134 - 214
9	9	chain 'H' and (resid 1 through 64 )	H	B	1 - 64	1 - 64
10	10	chain 'H' and (resid 65 through 138 )	H	B	65 - 138	65 - 138
11	11	chain 'H' and (resid 139 through 235 )	H	B	139 - 235	139 - 232
12	12	chain 'A' and (resid 1 through 76 )	A	C	1 - 76	1 - 76
13	13	chain 'A' and (resid 77 through 141 )	A	C	77 - 141	77 - 141
14	14	chain 'A' and (resid 142 through 213 )	A	C	142 - 213	142 - 213
15	15	chain 'B' and (resid 1 through 17 )	B	D	1 - 17	1 - 17
16	16	chain 'B' and (resid 18 through 40 )	B	D	18 - 40	18 - 40

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