PDB-9blx: Rhesus macaque ITS111.01 Fab in complex with SIV MPER peptide

ID or keywords:

Entry

Database: PDB / ID: 9blx

Title

Rhesus macaque ITS111.01 Fab in complex with SIV MPER peptide

Components

Envelope glycoprotein gp160
ITS111.01 Heavy
ITS111.01 Light

Keywords

IMMUNE SYSTEM/Viral Protein / Fab / MPER / membrane-proximal external region / HIV-1 / gp41 / IMMUNE SYSTEM / SIV / IMMUNE SYSTEM-Viral Protein complex

Function / homology

Function and homology information

membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function

Biological species

Macaca mulatta (Rhesus monkey)

Simian immunodeficiency virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Gorman, J. / Ahmadi, M. / Kwong, P.D.

Funding support

United States, 1items

Citation

Journal: Cell Rep / Year: 2025
Title: Isolation and structure of broad SIV-neutralizing antibodies reveal a proximal helical MPER epitope recognized by a rhesus multi-donor class.
Authors: Gorman, J. / Du, R. / Lai, Y.T. / Ahmadi, M.S. / King, H.A.D. / Song, K. / Manalang, K. / Gonelli, C.A. / Schramm, C.A. / Cheng, C. / Nguyen, R. / Ambrozak, D. / Druz, A. / Shen, C.H. / ...

History

Deposition	May 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9blx.cif.gz	565.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9blx.ent.gz	428.1 KB	Display	PDB format
PDBx/mmJSON format	9blx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9blx_validation.pdf.gz	482.7 KB	Display	wwPDB validaton report
Full document	9blx_full_validation.pdf.gz	491.3 KB	Display
Data in XML	9blx_validation.xml.gz	44.2 KB	Display
Data in CIF	9blx_validation.cif.gz	59.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/9blx ftp://data.pdbj.org/pub/pdb/validation_reports/bl/9blx	HTTPS FTP

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Related structure data

Related structure data	9bnsC 9bp1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5)

Deposited unit

H: ITS111.01 Heavy

L: ITS111.01 Light

A: ITS111.01 Heavy

B: ITS111.01 Light

I: Envelope glycoprotein gp160

G: Envelope glycoprotein gp160

hetero molecules

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

1

H: ITS111.01 Heavy

L: ITS111.01 Light

G: Envelope glycoprotein gp160

hetero molecules

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

2

A: ITS111.01 Heavy

B: ITS111.01 Light

I: Envelope glycoprotein gp160

hetero molecules

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

Unit cell

Length a, b, c (Å)	166.865, 118.834, 66.541
Angle α, β, γ (deg.)	90.000, 104.705, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y

Components on special symmetry positions

ID	Model	Components
1	1	L-392- HOH
2	1	L-421- HOH
3	1	L-427- HOH
4	1	B-490- HOH

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Protein/peptide , 1 types, 2 molecules IG

#3: Protein/peptide	Envelope glycoprotein gp160 Mass: 3445.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus / References: UniProt: A0A4Y5TJX4

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Antibody , 2 types, 4 molecules HALB

#1: Antibody	ITS111.01 Heavy Mass: 24462.385 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody	ITS111.01 Light Mass: 23365.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 477 molecules

#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 3.11 Å³/Da / Density % sol: 60.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MgCl2 25% PEG 400 20% PEG 3350 0.1M Tris-HCl pH 8.5 (glycerol for cryoprotectant)

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.96→40 Å / Num. obs: 85905 / % possible obs: 96.8 % / Redundancy: 3.9 % / B_iso Wilson estimate: 25.17 Å² / R_pim(I) all: 0.108 / R_rim(I) all: 0.229 / Net I/σ(I): 8.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.96-2.03	2.2	0.477	3569	0.708	0.91	0.341	0.59	0.908	80.9
2.03-2.07	2.3	0.476	3817	0.76	0.929	0.329	0.582	0.918	85.9
2.07-2.11	2.5	0.465	3950	0.709	0.911	0.316	0.566	0.92	88.8
2.11-2.15	2.7	0.422	4030	0.778	0.936	0.284	0.512	0.884	92
2.15-2.2	2.9	0.417	4191	0.792	0.94	0.268	0.498	0.913	94.6
2.2-2.25	3.2	0.417	4307	0.797	0.942	0.26	0.494	0.893	96.6
2.25-2.31	3.4	0.402	4291	0.827	0.952	0.242	0.471	0.894	98.1
2.31-2.37	3.7	0.389	4386	0.849	0.958	0.225	0.451	0.893	99
2.37-2.44	4	0.382	4427	0.867	0.964	0.215	0.439	0.907	99.9
2.44-2.52	4.3	0.382	4431	0.874	0.966	0.209	0.437	0.911	100
2.52-2.61	4.5	0.356	4426	0.901	0.974	0.19	0.405	0.96	100
2.61-2.71	4.6	0.343	4446	0.884	0.969	0.18	0.388	1.002	100
2.71-2.84	4.7	0.289	4418	0.91	0.976	0.151	0.327	1.015	100
2.84-2.99	4.7	0.26	4419	0.907	0.975	0.136	0.295	1.015	100
2.99-3.17	4.7	0.232	4441	0.923	0.98	0.121	0.263	1.021	100
3.17-3.42	4.7	0.212	4446	0.904	0.974	0.11	0.24	1.013	100
3.42-3.76	4.7	0.193	4468	0.94	0.984	0.1	0.218	0.963	100
3.76-4.31	4.7	0.165	4441	0.954	0.988	0.086	0.187	0.831	100
4.31-5.42	4.7	0.149	4470	0.947	0.986	0.078	0.169	0.738	100
5.42-40	4.6	0.157	4531	0.945	0.986	0.083	0.178	0.7	99.8

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Processing

Software

Name	Version	Classification
PHENIX	dev_5278	refinement
SCALEPACK		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→33.94 Å / SU ML: 0.2149 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2044	2000	2.63 %
R_work	0.178	74080	-
obs	0.1786	76080	84.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→33.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6870	0	51	472	7393

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	7105
X-RAY DIFFRACTION	f_angle_d	1.0412	9665
X-RAY DIFFRACTION	f_chiral_restr	0.0673	1084
X-RAY DIFFRACTION	f_plane_restr	0.0087	1228
X-RAY DIFFRACTION	f_dihedral_angle_d	14.7338	2538

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 (%)
1.96-2.01	0.2964	59	0.2256	2180	X-RAY DIFFRACTION	35.2
2.01-2.06	0.2532	83	0.2248	3073	X-RAY DIFFRACTION	49.76
2.07-2.13	0.2729	105	0.2137	3897	X-RAY DIFFRACTION	62.56
2.13-2.19	0.2168	125	0.2083	4637	X-RAY DIFFRACTION	74.87
2.19-2.27	0.2592	145	0.2039	5382	X-RAY DIFFRACTION	86.39
2.27-2.36	0.2486	157	0.194	5806	X-RAY DIFFRACTION	93.89
2.36-2.47	0.249	165	0.1857	6103	X-RAY DIFFRACTION	97.83
2.47-2.6	0.2299	166	0.1829	6156	X-RAY DIFFRACTION	99.11
2.6-2.76	0.2094	169	0.1761	6222	X-RAY DIFFRACTION	99.46
2.76-2.98	0.2222	166	0.1767	6183	X-RAY DIFFRACTION	99.28
2.98-3.28	0.1856	167	0.1671	6172	X-RAY DIFFRACTION	99.2
3.28-3.75	0.1892	166	0.1679	6169	X-RAY DIFFRACTION	98.6
3.75-4.72	0.1609	163	0.1489	6038	X-RAY DIFFRACTION	96.33
4.72-33.94	0.1942	164	0.1903	6062	X-RAY DIFFRACTION	95.52

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	0.964297682149	-0.298107417041	0.031164940501	1.05772980665	-0.415729129058	1.31082749518	0.0533280804356	0.112472297727	0.0821641541117	-0.0700645495475	0.0123561001634	0.10114432506	-0.207807723676	-0.343666002555	-0.0481652600496	0.170495764663	0.0807362566011	0.0351644478956	0.259005081144	0.0287008202212	0.185514544087	-42.8921242137	26.0012898629	29.3226267482
2	1.78819661195	-0.830577672889	-0.240959907493	2.55673120856	0.38678486	1.10026123409	-0.0942575995187	0.210225683417	0.00457679630808	-0.142822604523	0.0953967364289	-0.0419702968613	-0.0478811779773	-0.0172950973907	0.0081768616597	0.222098342787	0.0288070334022	0.0266500398158	0.268687416273	0.037353947014	0.163429646724	-26.1217217334	30.050354183	0.935681078457
3	1.43939328437	0.075549282944	-0.235128800641	1.05663689174	-0.603216480094	1.11719144439	0.0792518679925	-0.105077990758	0.109919140262	0.119561865074	-0.0164204073013	-0.00469246033607	-0.16431289395	0.030744411513	-0.0640903325249	0.12890112443	0.00120308006624	0.00732228394022	0.120276516837	-0.0198737071927	0.136153019937	-22.0781976643	18.6785401568	33.4524634132
4	2.11455307876	0.408851358153	0.279575704032	1.93260666578	0.180411458704	2.23139682419	-0.0649692100928	0.195991119254	0.388777009424	-0.0890914832052	-0.105089422251	-0.207258063889	-0.317349104939	0.245542170097	0.153100885029	0.202628785826	0.0096945936942	0.0177723297263	0.221044964634	0.0717237012097	0.264293769418	-12.4622668198	37.6620801724	3.50364880129
5	0.771322524478	-0.286241030485	-0.0691372862206	1.43197617101	0.533112745678	1.07615801364	0.0209005349133	-0.131915174706	-0.0608757338126	0.0376137795698	0.101612267812	-0.205557401111	0.171390287755	0.283846871579	-0.0895284495751	0.174821418494	0.0727163763572	-0.0201163763686	0.216058922816	-0.00480521277149	0.175988326992	-42.7633157745	52.4373626233	-5.12330017678
6	0.450569709738	-0.0140134215051	0.141364226285	0.99201287358	-0.713581570304	1.09304085386	0.228195457532	0.400788414214	0.0674039326147	-0.598078473736	-0.265708688912	-0.0580815935022	-0.293404336663	-0.12735881572	0.00570536324899	0.546269192694	0.266646385128	0.0148693447086	0.417612066459	0.0156731047379	0.209396063226	-44.3275234344	47.0194968841	-37.2927902448
7	0.85303146433	-0.115488782398	0.587239256095	0.679711264633	0.213569239397	1.30452035981	0.0581027237508	-0.14509247619	-0.166821156025	0.0884866116705	0.0761603161595	0.0861711839142	0.17468564532	-0.172808016682	-0.110507568682	0.185436443233	0.00116241849396	-0.00313788572355	0.19095069738	0.056112205402	0.215547064196	-64.0502822733	55.7003182937	-10.9264564461
8	0.346980261873	-0.218076630886	-0.33746762847	0.355133093835	0.153497960848	0.32775617654	0.504080659457	0.61938061684	-0.552584976024	-0.38780752758	-0.15984062247	0.122701746611	0.560489167578	0.438965575624	0.419117778143	0.527153652598	0.612467720149	-0.280189452119	0.538543778083	-0.568777346154	0.63145063555	-55.9488951186	37.2909058277	-41.4118074795
9	3.59360880749	2.44756557631	-0.32903799891	6.50977543032	0.308023536241	3.67598621523	0.226210751228	-0.364806219299	-0.0218574435352	0.328452632605	0.079230771755	-0.199466937918	-0.0353295277587	0.156299326235	-0.0579041120817	0.264833147112	0.0701799027537	-0.00797989471477	0.346926014727	-0.075956940175	0.227670264828	-47.2165146084	62.2560527858	10.6415365056
10	3.24860352311	1.23102782217	-0.498977462371	4.56665741848	0.370255508834	4.25021379237	0.0997918555688	-0.065519446603	0.181266981048	0.0537880742915	0.076087064267	0.359257914107	-0.174435553006	-0.263210877819	0.0513292367995	0.209071904464	0.0382365755982	0.0650815884158	0.324819104059	0.0818680777089	0.232943312569	-47.4689010407	16.4726205843	45.2132670085

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 'H' and (resid 1 through 113 )	H	A	1 - 113	1 - 123
2	2	chain 'H' and (resid 114 through 216 )	H	A	114 - 216	124 - 226
3	3	chain 'L' and (resid 1 through 113 )	L	B	1 - 113	1 - 113
4	4	chain 'L' and (resid 114 through 213 )	L	B	114 - 213	114 - 213
5	5	chain 'A' and (resid 1 through 112 )	A	C	1 - 112	1 - 122
6	6	chain 'A' and (resid 113 through 214 )	A	C	113 - 214	123 - 224
7	7	chain 'B' and (resid 1 through 113 )	B	D	1 - 113	1 - 113
8	8	chain 'B' and (resid 114 through 210 )	B	D	114 - 210	114 - 210
9	9	chain 'I' and (resid 661 through 674 )	I	E	661 - 674	2 - 15
10	10	chain 'G' and (resid 661 through 674 )	G	F	661 - 674	2 - 15

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-Antibody , 2 types, 4 molecules HALB

-Non-polymers , 3 types, 477 molecules

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Protein/peptide , 1 types, 2 molecules IG

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Antibody , 2 types, 4 molecules HALB

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Non-polymers , 3 types, 477 molecules

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