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- PDB-9e7d: Crystal structure of HIV-1 RRE SLII A31C mutant in complex with F... -

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Basic information

Entry
Database: PDB / ID: 9e7d
TitleCrystal structure of HIV-1 RRE SLII A31C mutant in complex with Fab BL3-6
Components
  • BL3-6 Fab heavy chain
  • BL3-6 Fab light chain
  • Rev response element SLIIc
KeywordsRNA / HIV-1 / Replication / Fab / Chaperone / Rev response element
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsOjha, M. / Koirala, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentNA United States
CitationJournal: To Be Published
Title: Crystal structure of HIV-1 RRE SLII A31C mutant in complex with Fab BL3-6
Authors: Ojha, M. / Koirala, D.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Rev response element SLIIc
C: Rev response element SLIIc
H: BL3-6 Fab heavy chain
L: BL3-6 Fab light chain
A: BL3-6 Fab heavy chain
B: BL3-6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)142,7996
Polymers142,7996
Non-polymers00
Water00
1
R: Rev response element SLIIc
H: BL3-6 Fab heavy chain
L: BL3-6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)71,3993
Polymers71,3993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Rev response element SLIIc
A: BL3-6 Fab heavy chain
B: BL3-6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)71,3993
Polymers71,3993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.874, 75.871, 83.516
Angle α, β, γ (deg.)63.170, 71.850, 77.750
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "H"
d_1ens_2chain "B"
d_2ens_2chain "L"

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CYS / End label comp-ID: CYS

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1AE3 - 2283 - 228
d_2ens_1HC3 - 2283 - 228
d_1ens_2BF1 - 2151 - 215
d_2ens_2LD1 - 2151 - 215

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.409132154952, -0.766828256111, -0.494555664627), (-0.759280382524, -0.014492169742, 0.650602242334), (-0.50606736755, 0.64168871164, -0.576308438993)0.77247497553, 5.0010526351, -93.8715718076
2given(-0.402747452378, -0.768307489933, -0.497491799447), (-0.76244438248, -0.0191210189516, 0.646771173027), (-0.506431686634, 0.639795270026, -0.578090788047)1.07667050583, 5.04059729437, -93.9232117145

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Components

#1: RNA chain Rev response element SLIIc


Mass: 23237.883 Da / Num. of mol.: 2 / Mutation: A31C / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 902798
#2: Antibody BL3-6 Fab heavy chain


Mass: 24766.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody BL3-6 Fab light chain


Mass: 23394.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.2 M Ammonium nitrate, 20% PEG 3,350, pH 6.2 / PH range: 6.0-6.5 / Temp details: Liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.1→34.2 Å / Num. obs: 21022 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.779 / Net I/σ(I): 1.5
Reflection shellResolution: 3.106→3.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.446 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3048 / CC1/2: 0.319 / Rpim(I) all: 0.934 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→34.2 Å / SU ML: 0.497 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.7362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.329 962 4.8 %
Rwork0.2458 19098 -
obs0.2497 20060 73.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.5 Å2
Refinement stepCycle: LAST / Resolution: 3.11→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 3082 0 0 9736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009710254
X-RAY DIFFRACTIONf_angle_d1.364414620
X-RAY DIFFRACTIONf_chiral_restr0.06311758
X-RAY DIFFRACTIONf_plane_restr0.01151326
X-RAY DIFFRACTIONf_dihedral_angle_d17.80174156
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EAX-RAY DIFFRACTIONTorsion NCS0.45655202216
ens_2d_2FBX-RAY DIFFRACTIONTorsion NCS0.415650505042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.11-3.270.37271420.30022764290674.84
3.27-3.470.37921510.3081287876.96
3.47-3.480.643810.2733422.44
3.81-4.120.36621250.2702257287.71
4.12-4.710.35521740.2382347893.93
4.71-5.930.29041780.228369399.28
5.93-34.20.27991910.2043367999.33
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.441220378750.8320952768790.3743557123270.687296538083-0.272950713891.225251739320.0924318695509-0.653866646931-1.11042535126-0.05296217712680.0200585202746-0.4428020883020.3689228875780.168966309440.3060957074990.869590691648-0.3093588332750.05149339689360.8080781784650.5216020592251.58921746496-44.8640847505-1.37030158183-5.96588740412
21.24980970457-0.815575963494-0.7077780969231.422183043931.45246674711.50531605381-0.0755777747178-0.709752609391-1.313938698390.214786431485-0.03791748442160.07507565866790.01059629603050.2570209052810.21846593911.29066617004-0.185250971680.4512788325161.056346249750.2674320439932.12474805256-25.1293349085-14.4671374665-11.2075813932
31.04369195753-0.207749932995-0.8239630541640.06546888268670.1706381540790.650569436693-0.35751464001-1.06645161256-1.502095886070.4498948952770.06053364324790.2977996134230.116919662228-0.03604428301970.1372513807631.197939074430.1909286020290.5823101441721.021599628050.6851229662862.21832239773-35.3272944567-22.0814510425-3.13483648771
41.987165892750.2194107141640.491859054660.07930301955160.2425343153210.8271256222210.122396524976-0.874907904026-1.27172390164-0.129413723885-0.2265101882880.2959412956050.679629345348-0.257802388204-0.01276396591290.14483015548-0.4605610962680.2599911197320.4425195674690.6229542086851.40799390631-26.79443496993.4876996384-0.571700631269
51.17350905213-0.235091880495-0.6391857843290.04900363709790.1169885949630.3790946617440.1397352742840.4079876861860.629145299136-0.378801149634-0.128323464003-0.446851311240.2019919766090.377111576641-0.1884660570921.87003171052-0.03955014508230.6510479728021.676034878260.3292018415352.52000881651-16.161104041778.665079162-46.3290955358
61.36299404356-0.698973507298-0.649213826890.4615341539870.237224595370.5989554769890.1718438721760.261745572041.43686710219-0.08390358384630.283548702031-0.841079631954-0.6674080364410.783357593317-0.005869177117121.20532360398-0.3609887340160.06674432495631.019813513930.4340796151341.1593298926-32.144776860281.5991654373-42.9546427633
74.9565978370.725451704117-0.8927703037233.34458598723-2.651989807292.125181688020.0498696313943-0.2780745786370.343127775198-0.1444342767270.3178747339650.317683820919-0.2966181880170.335548134132-0.4951428714070.0180336809418-0.008404259212360.1605111656070.06195901058430.286871983210.6650238137325.6955206504219.7674297522-25.8643555953
83.141243456240.712216194605-1.262677335071.412990374050.2942972674611.841054344820.0751122855959-0.420066380311-0.1449205400220.111661370277-0.04624231010070.0835020294901-0.03787777766140.1487655204930.01394420209220.141756852567-0.201599086428-0.1037455492270.263877060780.3785632157070.5037788210873.6087492366417.3531350788-14.1502199456
91.33896959134-0.7245389644270.08639460814240.8006285704980.1040514745570.644832626447-0.01981666783060.183737256909-0.118778159482-0.131189048163-0.2141337083370.169745820925-0.00984123310523-0.0539424394597-0.161165325213-0.2277842821770.110212916590.0791242889295-0.06687317975160.121191823810.417678090717-6.9817443526415.9999875817-22.7421530061
102.13714095336-0.2756142851160.1628475161280.8535409803130.6871356675272.041894278060.0869247742880.0523580502684-0.3202936735110.0148517083345-0.0716316090908-0.1572329402620.1406074775470.271271364754-0.1015988439080.01187172061790.077390542648-0.09930710013660.1176232360190.06711379979730.5806253554441.9005274151210.7394561745-21.0910792875
113.74549479237-1.07877564501-0.1355017493713.00316237331.705033126374.03458221110.1100563007-0.0204452585186-0.355160454345-0.5671238498720.1833010378250.06232151731120.3635092335720.0249814614582-0.1821300596280.311186161094-0.1485095883120.02485887495140.06324023559550.1773163930020.466106501151-2.3579226435317.5399533454-28.9696891934
127.201095397162.37823446509-3.588680009454.89284660388-1.553711153244.33548843370.103878915999-0.59608490481-0.1133203534280.370431440697-0.1166122027110.122725124826-0.1055792538920.158787093933-0.1493093757060.05393936658260.1033031649390.1575572357320.2142062169490.3121575570630.347157105329-7.6557194989724.4051421931-9.76277581786
131.23270547491-0.803727136425-0.6035828630870.949247203128-0.3843306722831.812882500690.02161932604590.111243421742-0.066995691002-0.200258714897-0.048517559939-0.04983053225290.2916715349160.0681457831666-0.104651483330.3522490194560.159460318095-0.0126831314250.1134453335740.003807354218120.216573248115.7675365686225.5850795541-44.015591469
140.9219380815370.115651814140.3959371937431.28848960468-0.1497332134832.09000827479-0.04042686352120.3193824340940.311617174892-0.2611458903320.09936523662960.348545657301-0.310437607955-0.138393134294-0.07453357054660.6728522470390.3091935735580.02885634878160.3338703793930.2602335429490.2638238327381.0756372026643.5338129568-55.531887654
151.122964561360.240145110026-0.1968871528560.7618021875750.2660736925130.7653868770680.2523883326660.1406802999330.00642550903656-0.17487681282-0.03126948244680.0811927312716-0.0919714420905-0.07495209108370.2877052178220.1412246572520.292472372284-0.0304900553461-0.1096617852390.1039078926930.09627775231464.4010929895838.5570686724-47.1815068967
162.184808466191.25942136549-0.6152707622673.30311096285-0.4404353797291.2503801578-0.01868912495160.505951846926-0.126244336546-0.277761868722-0.27233138071-0.424648573841-0.04701908761980.08979654838390.1547656779410.6836511935250.0862436293387-0.1125965431170.3518204830040.2071824409170.26377330792311.841552488241.5055051114-53.7390290338
177.791459272274.15408004405-1.026566138843.640545914370.7286394353112.395837046270.041232735810.0556998856478-0.450105203087-0.356116355383-0.204480204842-0.203788020428-0.160425311923-0.1141216259170.3632762181880.442678184463-0.156873842489-0.1670522913210.6510544082180.2633125579760.340707938063-20.506183878633.8212224897-25.952308009
180.802731733234-0.647819366431-0.1563335524310.891008875090.2669791192560.510214115082-0.0300465590918-0.105593511705-0.03375625439850.04679624114030.1549411117470.24119298454-0.258066437546-0.1801285671280.400550016888-0.06113999964110.5781035774710.2362864187480.02603568319530.1912018537830.525648088062-14.697095822733.7675335574-21.1482478336
190.270108989059-0.06611976428110.1411057278480.1363277815730.3366505339911.163240016460.0981474569270.222324992909-0.0216192051385-0.268106829602-0.1464271512360.1859003943830.1738242777520.1692289523790.01305755189440.5199605978370.212879827199-0.2479264921530.02420635818890.3726348896630.401186436824-7.2442590144237.8489710108-54.0851893957
203.6600703795-0.989863507113-2.926647656752.406092651683.258600606745.185542618580.6552759758830.467356784860.148339536207-0.806908529053-0.4047351088130.256070138794-0.756695903955-0.707793348235-0.06933672766751.008423929670.127587806386-0.3214481636230.7490283086420.1242328528230.45437696378-12.785874390242.9725804919-60.778858757
215.43774497557-2.88198826044-0.1137524518084.537221031022.468423349534.340729879720.251185837935-0.333552250144-0.5433112965770.627529048938-0.3981750885980.392523356033-0.22420182939-0.0326290563358-0.1447417502910.541601802156-0.4775110788990.2106346092850.5414595879670.05584783983510.338030207058-47.535381717139.6963408656-31.9792941482
223.43941796578-1.672635310910.6095570986271.979924661380.789939204551.169106033610.1525576730870.331987468827-0.1690910608390.0575812659959-0.2932667523930.193313751136-0.199534259719-0.382302895613-0.09196219638120.192048658455-0.0922861474389-0.001058707276270.4442960200850.06596500308850.105822765465-50.795556420948.621250488-39.4322976758
231.49396559687-0.418485921893-0.4237389443030.5672851706250.2855389728820.6055695905790.118432434614-0.03970284798120.172651710805-0.08843211110640.0525950147181-0.128733420432-0.05374863255070.02703248074080.190042884644-0.04458839121960.2981807682280.4147299589070.1560034277140.0247199993620.0483195793491-41.16054303351.4123196126-30.0193371755
243.50517909518-0.3692996312890.425787660290.525864968163-0.2710841316471.832674944620.02917865018060.1995420210180.08373793602240.0338089663149-0.04162579096190.0305440320261-0.0194823363561-0.117905070931-0.2376456512870.152667231305-0.3277792080670.2200655956710.29469186296-0.125310758530.149775836554-41.627049735445.7755558493-38.7897680243
251.98890498464-0.98855894144-1.631887077561.481865696611.168581954792.65985912551-0.285699307192-0.05488465415260.1207709955890.0158089792178-0.0485333624335-0.09452179438260.5239933962970.155604265341-0.100510719750.178139546647-0.1721837071860.225761752160.449020596466-0.01693504601410.326928740597-41.106026399243.9027927334-27.6976350045
263.81295898176-0.1571718677650.5342093987173.048732506912.192319528254.10965776808-0.09495328509180.775141857261-0.0214717200816-0.72158485432-0.1542118662790.0615782587995-0.748749979665-0.01777583413040.431369443070.600628080751-0.26780372423-0.1375899382590.5071461569310.00997870757220.249994016534-53.859287054560.2405907911-31.6089511285
270.715565278944-0.344298151304-0.2792541250710.7917262695150.1474433761470.1671473650810.0714513138668-0.270528506527-0.0991859104641-0.0430462988756-0.0585601766376-0.2042428291470.128129032629-0.0618212621926-0.06395570152070.199629451838-0.1535653019860.05507203734550.539852474527-0.00754149419970.0884061888994-42.908347493927.9933915319-18.002189004
281.26301631180.522091249911-0.2861924642481.81033162402-0.3034221263330.2241241578860.140293495443-0.586250128749-0.1396170104070.7101133048290.1021500821850.3023458146240.04407355102330.0452058532185-0.1151700997310.4694884979060.01061649444070.02775321052940.6591834252560.2600535676740.141576292432-48.75346293723.92051893732.95517729239
290.7961482038780.16734040982-0.1489142491460.5025257388780.1682606139320.4546637691580.072152018063-0.0631449002569-0.120194939126-0.01744597178260.0560897640970.113830414331-0.001847678030.1014646349260.2216985469140.0519932919549-0.4460236319980.00548311628610.5104230129510.3231264756460.162932374191-50.721827103526.6538628991-6.7701360216
301.308756326690.120042845679-0.629204314721.88042908150.5450201560951.02577921906-0.247455071446-0.131172040743-0.1897509393460.403353425870.2399065507680.03009120243250.0161951853935-0.0008453359006750.06107442593190.49912813699-0.121249914201-0.2447161946720.7100679210490.4344873430460.365580727476-52.51147167116.6365019745-4.91605145595
312.389104334661.31653479530.02248033081193.155952938670.4819576826270.666348829732-0.0553651598668-0.293594137764-0.02056884875260.2914362001470.0896472760551-0.3230090961450.111410467480.1665489356850.03229263998390.599164919008-0.30634888162-0.388914078150.609064728694-0.004209504967760.322261143779-47.794829300659.5198220854-9.94880903226
320.668651632627-0.3134971574060.1614012081081.28303446188-0.154735025330.0538293024448-0.101186314669-0.0730142665620.1806096653260.303009324067-0.167044454563-0.067715984148-0.1550563276080.096499706059-0.2380825927430.706879026811-0.45313432467-0.1506072848150.2505870732550.1633910773110.20148114946-52.38607380858.1267876867-15.6011661304
330.249832251833-0.121862084137-0.08431192061590.2305144683220.2094541476220.5250856170310.203817157164-0.0934570499421-0.003170146146290.04106082583520.0489774888615-0.17482143071-0.04411711879230.4487709653820.8694858517810.556185058755-0.3668716064890.009052202216050.8777194792220.174244286531-0.03785745069-41.803573998431.22982832572.28924525772
343.79461526756-3.590789291592.230715098396.59958456942-0.1019301972512.87425518281-0.120982770905-0.47014105088-0.132220725270.6928973967950.2787755374470.1932733909280.5106413026940.42725755139-0.279589356650.90200440808-0.2449498141-0.06862611232510.9453066980390.2566044882080.29835474742-40.17221513731.200684949812.2540278739
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'R' and (resid 1 through 10 )RA1 - 10
22chain 'R' and (resid 11 through 25 )RA11 - 25
33chain 'R' and (resid 26 through 35 )RA26 - 35
44chain 'R' and (resid 36 through 72 )RA36 - 72
55chain 'C' and (resid 1 through 30 )CB1 - 30
66chain 'C' and (resid 31 through 72 )CB31 - 72
77chain 'H' and (resid 3 through 20 )HC3 - 201 - 18
88chain 'H' and (resid 21 through 36 )HC21 - 3619 - 34
99chain 'H' and (resid 37 through 67 )HC37 - 6735 - 65
1010chain 'H' and (resid 68 through 86 )HC68 - 8666 - 84
1111chain 'H' and (resid 87 through 102 )HC87 - 10285 - 100
1212chain 'H' and (resid 103 through 115 )HC103 - 115101 - 113
1313chain 'H' and (resid 116 through 136 )HC116 - 136114 - 134
1414chain 'H' and (resid 137 through 157 )HC137 - 157135 - 155
1515chain 'H' and (resid 158 through 200 )HC158 - 200156 - 198
1616chain 'H' and (resid 201 through 228 )HC201 - 228199 - 226
1717chain 'L' and (resid 1 through 26 )LD1 - 261 - 26
1818chain 'L' and (resid 27 through 114 )LD27 - 11427 - 114
1919chain 'L' and (resid 115 through 189 )LD115 - 189115 - 189
2020chain 'L' and (resid 190 through 215 )LD190 - 215190 - 215
2121chain 'A' and (resid 3 through 20 )AE3 - 201 - 18
2222chain 'A' and (resid 21 through 36 )AE21 - 3619 - 34
2323chain 'A' and (resid 37 through 67 )AE37 - 6735 - 65
2424chain 'A' and (resid 68 through 86 )AE68 - 8666 - 84
2525chain 'A' and (resid 87 through 102 )AE87 - 10285 - 100
2626chain 'A' and (resid 103 through 115 )AE103 - 115101 - 113
2727chain 'A' and (resid 116 through 136 )AE116 - 136114 - 134
2828chain 'A' and (resid 137 through 157 )AE137 - 157135 - 155
2929chain 'A' and (resid 158 through 200 )AE158 - 200156 - 198
3030chain 'A' and (resid 201 through 228 )AE201 - 228199 - 226
3131chain 'B' and (resid 1 through 26 )BF1 - 261 - 26
3232chain 'B' and (resid 27 through 114 )BF27 - 11427 - 114
3333chain 'B' and (resid 115 through 189 )BF115 - 189115 - 189
3434chain 'B' and (resid 190 through 215 )BF190 - 215190 - 215

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