PDB-9e7g: Crystal structure of HIV-1 RRE SLII G34C mutant in complex with F...

ID or keywords:

Entry

Database: PDB / ID: 9e7g

Title

Crystal structure of HIV-1 RRE SLII G34C mutant in complex with Fab BL3-6

Components

BL3-6 Fab heavy chain
BL3-6 Fab light chain
Rev Response Element SLII

Keywords

RNA / HIV-1 / Replication / Fab / Chaperone / Rev response element

Function / homology

: / RNA / RNA (> 10)

Function and homology information

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Ojha, M. / Koirala, D.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of HIV-1 RRE SLII G34C mutant in complex with Fab BL3-6
Authors: Ojha, M. / Koirala, D.

History

Deposition	Nov 1, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 28, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9e7g.cif.gz	318.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9e7g.ent.gz	215.6 KB	Display	PDB format
PDBx/mmJSON format	9e7g.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/e7/9e7g ftp://data.pdbj.org/pub/pdb/validation_reports/e7/9e7g	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #32 - Aug 2002 Chaperones similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
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#146 - Feb 2012
Aminoglycoside Antibiotics
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#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
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#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#32 - Aug 2002
Chaperones
similarity (1)
#21 - Sep 2001
Antibodies
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#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
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#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

H: BL3-6 Fab heavy chain

L: BL3-6 Fab light chain

R: Rev Response Element SLII

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

1

Idetical with deposited unit
defined by author
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	90.785, 106.630, 187.331
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222
Space group name Hall	I22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1/2 #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Antibody	BL3-6 Fab heavy chain Mass: 24766.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	BL3-6 Fab light chain Mass: 23394.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: RNA chain	Rev Response Element SLII Mass: 23221.883 Da / Num. of mol.: 1 / Mutation: G34C / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 902798
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: 3.18 Å³/Da / Density % sol: 61.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane pH 8.8, 16% PEG 3350 and 0.3% Ethanol

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 3→46.83 Å / Num. obs: 35117 / % possible obs: 99.8 % / Redundancy: 13.6 % / B_iso Wilson estimate: 84.16 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.115 / Net I/σ(I): 14.6
Reflection shell	Resolution: 3→3.05 Å / R_merge(I) obs: 1.671 / Mean I/σ(I) obs: 1 / Num. unique obs: 889 / CC_1/2: 0.795 / % possible all: 96.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→38.77 Å / SU ML: 0.5048 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2337	3502	9.97 %
R_work	0.1897	31615	-
obs	0.1941	35117	99.36 %

Solvent computation

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

Displacement parameters

B_iso mean: 144.41 Å²

Refinement step

Cycle: LAST / Resolution: 3→38.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3327	1540	0	0	4867

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	5126
X-RAY DIFFRACTION	f_angle_d	1.152	7308
X-RAY DIFFRACTION	f_chiral_restr	0.056	879
X-RAY DIFFRACTION	f_plane_restr	0.0101	663
X-RAY DIFFRACTION	f_dihedral_angle_d	18.3216	1339

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 (%)
3-3.04	0.5615	133	0.4476	1181	X-RAY DIFFRACTION	94.67
3.04-3.08	0.406	143	0.3918	1287	X-RAY DIFFRACTION	98.83
3.08-3.13	0.4463	140	0.3708	1234	X-RAY DIFFRACTION	99.13
3.13-3.17	0.3309	142	0.3357	1273	X-RAY DIFFRACTION	98.61
3.17-3.23	0.3005	144	0.2881	1248	X-RAY DIFFRACTION	99.15
3.23-3.28	0.3195	140	0.2685	1242	X-RAY DIFFRACTION	99.42
3.28-3.34	0.3007	143	0.2357	1313	X-RAY DIFFRACTION	99.39
3.34-3.41	0.2855	143	0.2533	1253	X-RAY DIFFRACTION	99.29
3.41-3.48	0.2367	135	0.231	1241	X-RAY DIFFRACTION	99.14
3.48-3.55	0.3044	143	0.2401	1269	X-RAY DIFFRACTION	99.37
3.55-3.63	0.2679	137	0.2364	1252	X-RAY DIFFRACTION	99.71
3.63-3.72	0.2415	132	0.2096	1261	X-RAY DIFFRACTION	99.71
3.72-3.82	0.2279	145	0.202	1277	X-RAY DIFFRACTION	99.79
3.82-3.94	0.2561	144	0.194	1276	X-RAY DIFFRACTION	99.65
3.94-4.06	0.2275	145	0.1792	1263	X-RAY DIFFRACTION	99.58
4.06-4.21	0.2348	139	0.1775	1262	X-RAY DIFFRACTION	99.72
4.21-4.38	0.1992	137	0.1541	1267	X-RAY DIFFRACTION	99.93
4.38-4.58	0.2015	144	0.1587	1285	X-RAY DIFFRACTION	99.93
4.58-4.82	0.2196	145	0.1445	1280	X-RAY DIFFRACTION	99.86
4.82-5.12	0.2058	137	0.154	1277	X-RAY DIFFRACTION	99.93
5.12-5.51	0.1968	134	0.1595	1271	X-RAY DIFFRACTION	100
5.51-6.06	0.2378	136	0.187	1275	X-RAY DIFFRACTION	99.93
6.07-6.94	0.2177	145	0.1914	1277	X-RAY DIFFRACTION	99.93
6.94-8.72	0.2158	140	0.1825	1265	X-RAY DIFFRACTION	100
8.73-38.77	0.1833	136	0.1382	1286	X-RAY DIFFRACTION	99.72

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	6.60373440639	1.55684198791	0.157760545842	8.12580279537	5.12755973441	3.27754347845	0.834059598865	1.35124466807	1.04246445609	2.18200791813	-2.50205018651	-1.74837621802	0.113649984874	2.82871901696	1.34997147725	2.76561901625	0.0163284127614	0.139470623976	1.57538161115	0.234009989962	1.35720559907	27.3581056945	10.6306448884	-13.8193106813
2	3.46782828276	2.04758573715	3.3804953437	7.45047343	0.349303303533	9.45036638857	-0.469438417951	0.632816476967	1.14709494807	0.278926404866	0.0664931014419	5.34372078009	-0.528075639398	-3.31280561798	0.51939945222	3.79880783518	0.311232846795	-0.932098173203	2.98316186493	-0.341918209235	5.12437892926	-2.75349188054	20.0788490594	-24.5181241051
3	3.27055066202	0.669090947023	3.75252303175	4.50402778078	1.24399951693	4.90260419186	-0.698120624619	1.19608201131	0.194902340243	-1.65337563669	0.411747681203	2.03521198865	0.28662782192	0.5137153801	0.21350506642	3.13678993578	-0.1938819256	-0.248367713336	2.04040556805	-0.248232249928	2.42122025506	15.0853103012	19.4783587378	-23.7576307037
4	0.491027985631	0.236908097789	-1.9070229865	0.136318174119	-0.557037717417	4.40115217781	0.0263971361835	-0.0750806718416	-0.399488749295	0.508650120014	-0.526043146807	0.0362825102757	0.965470872272	-0.174204631016	0.426787584748	1.03774305493	-0.145057896502	-0.0973190063529	0.729082465196	0.0696496855568	1.17440235092	24.4200994029	36.4032610815	-1.25992887652
5	0.522556223171	-0.634074920575	1.2432608049	3.77504209988	-0.632140957069	1.07596656398	1.20317818055	0.278864537339	-0.952568074855	1.08347748708	-0.72983677736	-0.185989756069	2.39980114074	0.0564551678284	0.101842195469	2.50599084836	0.0889874502048	0.0467974425189	1.13647348455	0.141095854769	1.85508185688	28.5120596781	10.8329862394	-9.1120291661
6	3.67930202393	-1.75263934322	-0.669432068739	2.4903240874	-0.52399524985	2.93172940543	0.343381673833	0.253997010668	0.203757631989	0.179939958147	0.930730441923	1.0129286196	0.153499905362	-2.31792924567	-0.963567064736	0.814737422763	-0.249881780918	-0.0393374556145	1.25630443076	0.0190210695539	1.0010261991	7.83653205616	51.4448177931	27.9333879502
7	4.07887532628	-0.765318775432	-0.0145137732454	2.10973232633	0.820187350179	6.34010185343	0.461945620412	-0.13289163114	-0.0708542240939	0.0656138349248	0.0806583443511	0.434413635132	0.215685198614	-1.3663432195	-0.181718411735	0.678412639359	-0.226295812943	0.0131878469115	0.966766072411	0.0685764822696	0.946233109553	11.5470859291	49.3932102741	18.8741279642
8	5.62971259072	-0.0836735275105	-1.52336509673	3.28848806404	1.40431801275	5.10964465839	0.434108098532	-1.37727673156	-0.232932336133	0.419039381993	0.0887579839784	-0.548769604575	0.964621200012	0.773991610672	-0.295280049458	0.826097370766	-0.225884773825	-0.0177351340852	0.841004859357	0.104071191483	1.1103110139	20.41638251	46.4520856119	28.5290956191
9	3.46775631496	0.274866225471	-0.201729378659	0.689709420405	0.31073587624	9.74526619196	0.651606637426	0.466950551984	-1.60815468315	0.0360693307074	0.565829961073	0.163786481455	1.51774967496	0.898421491106	-0.0969945836357	0.918106095307	-0.262380458472	-0.0409574000317	0.807330127173	0.136099138111	1.15236963027	16.6296903215	38.4756426884	17.9795879553
10	4.82242350932	0.156371227315	-0.123833861239	3.39441193096	-0.623971541522	6.82788445267	0.286936429482	0.119680789791	-0.394155902609	0.256351819423	-0.387417229417	-0.126108548265	0.732221063984	-0.9592635432	-0.0815621949327	0.814032078452	-0.317186722922	-0.00973754491763	1.1104475479	0.137535684363	0.968164120534	7.73941118182	42.6863588591	21.5329536641
11	5.475917632	-0.221179022104	-0.982821542242	1.8882697479	1.70904684503	7.23754953155	0.236021551078	-1.04170385679	-0.341762707171	0.861906395091	-0.328340876307	-0.182204710767	0.506406326891	-0.688475140331	-0.159223283779	0.812830795365	-0.303299021501	0.0402368231471	1.14237292634	0.141947029341	0.987469812374	14.5136739953	45.8272352946	29.9269138439
12	2.95755532578	-1.03657280516	-0.415779823361	1.42323392562	0.970205349087	2.92717915664	0.324127793551	-0.445147012667	0.401799402909	0.0012048622063	0.0635595729302	-0.0910396918657	-0.210484477797	-0.771579008568	-0.13047439191	0.783064853205	-0.269126870868	-0.036154520817	1.0404878814	0.00453297610312	0.983771659989	14.8735200218	54.1951272109	29.8557088825
13	3.70540306466	2.19683145793	-2.73964970841	4.28954343153	-2.03498214451	7.65247579366	0.28710656892	-0.860941976482	1.10676049947	0.317807693573	-0.0433908993483	-0.323640023086	-0.873841661026	-0.759072023116	-0.400279945495	0.857720105686	-0.192876322626	0.0911648896517	1.42229839323	-0.448421428121	1.29336782134	14.8616678267	71.0332935117	50.5663939633
14	3.13729068002	1.01819617275	-1.61096848612	5.26606678959	-0.957851641358	3.96405078606	-0.0727358614644	-1.23459889713	0.29717734513	0.612782660777	0.244637500303	-0.816910824684	-0.583944906984	-0.484727904002	-0.134627275675	1.05119172262	-0.224422573864	0.00309669980345	1.51239861708	-0.442076574096	1.15143294333	15.7349808022	68.4881757317	51.8223390751
15	1.66853744994	-0.904869028703	-0.146288798358	3.08756520156	-1.38015176656	6.54632805472	-0.0593507415488	-0.506221641432	0.7937145279	-0.375766784231	0.195496714496	0.352745876666	-1.63840925159	-1.43090097283	-0.148283071231	1.08309239373	-0.128337872013	0.214141804334	1.98783688474	-0.585971582436	1.35020912217	5.99060431354	70.0825933141	52.1008756751
16	7.68857978684	-1.11325742914	0.453557267971	3.37007182032	2.40110371125	6.1124691424	0.199386781734	-0.801011758443	0.181616929942	-0.00908324161341	-0.0990998612367	-0.177695161636	-0.102935818446	0.144180280553	-0.130154061607	0.656707991061	-0.211356471646	0.0355301021468	0.556571894574	0.082510360003	0.854143585023	34.2279691131	55.1209105065	22.5118076348
17	4.17453677749	-1.10781848999	-2.41337095179	1.65963596421	1.08577858202	5.89938141623	0.354267458302	-1.29354620511	0.517556520654	0.367055669837	-0.0777487211743	-0.206444045603	-0.271538593036	-0.204458237251	-0.314044672421	0.668204829284	-0.149743758437	-0.0684688519934	0.968650758461	-0.0920891949425	0.917402450701	27.3408510481	61.0733188576	38.6356698976
18	3.04146885113	0.294885243755	-2.77060484277	3.43289078278	-0.117382019608	5.65731933677	0.167146236768	-1.23457001399	0.0898316359948	0.726196366952	-0.0589430836454	-0.5313558633	0.124188931913	0.576258125676	-0.160033630727	1.05331384493	-0.151478447207	-0.0975717820155	1.7782580369	-0.333811842201	1.1406391609	26.698455456	64.5905546754	58.8760289584

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 'R' and (resid 1 through 10 )	R	C	1 - 10
2	2	chain 'R' and (resid 11 through 25 )	R	C	11 - 25
3	3	chain 'R' and (resid 26 through 40 )	R	C	26 - 40
4	4	chain 'R' and (resid 41 through 60 )	R	C	41 - 60
5	5	chain 'R' and (resid 61 through 72 )	R	C	61 - 72
6	6	chain 'H' and (resid 3 through 20 )	H	A	3 - 20	1 - 18
7	7	chain 'H' and (resid 21 through 42 )	H	A	21 - 42	19 - 40
8	8	chain 'H' and (resid 43 through 54 )	H	A	43 - 54	41 - 52
9	9	chain 'H' and (resid 55 through 67 )	H	A	55 - 67	53 - 65
10	10	chain 'H' and (resid 68 through 86 )	H	A	68 - 86	66 - 84
11	11	chain 'H' and (resid 87 through 102 )	H	A	87 - 102	85 - 100
12	12	chain 'H' and (resid 103 through 136 )	H	A	103 - 136	101 - 134
13	13	chain 'H' and (resid 137 through 177 )	H	A	137 - 177	135 - 175
14	14	chain 'H' and (resid 178 through 205 )	H	A	178 - 205	176 - 203
15	15	chain 'H' and (resid 206 through 228 )	H	A	206 - 228	204 - 226
16	16	chain 'L' and (resid 1 through 76 )	L	B	1 - 76	1 - 76
17	17	chain 'L' and (resid 77 through 129 )	L	B	77 - 129	77 - 129
18	18	chain 'L' and (resid 130 through 215 )	L	B	130 - 215	130 - 215

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