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- PDB-4qf1: Crystal structure of unliganded CH59UA, the inferred unmutated an... -

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Basic information

Entry
Database: PDB / ID: 4qf1
TitleCrystal structure of unliganded CH59UA, the inferred unmutated ancestor of the RV144 anti-HIV antibody lineage producing CH59
Components
  • CH59UA Fab fragment of heavy chain
  • Inferred unmutated ancestor (UA) of anti-HIV antibody CH59
KeywordsIMMUNE SYSTEM / anti-HIV antibody / gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWiehe, K. / Easterhoff, D. / Luo, K. / Nicely, N.I. / Bradley, T. / Jaeger, F.H. / Dennison, S.M. / Zhang, R. / Lloyd, K.E. / Stolarchuk, C. ...Wiehe, K. / Easterhoff, D. / Luo, K. / Nicely, N.I. / Bradley, T. / Jaeger, F.H. / Dennison, S.M. / Zhang, R. / Lloyd, K.E. / Stolarchuk, C. / Parks, R. / Sutherland, L.L. / Scearce, R.M. / Morris, L. / Kaewkungwal, J. / Nitayaphan, S. / Pitisuttithum, P. / Rerks-Ngarm, S. / Michael, N. / Kim, J. / Kelsoe, G. / Montefiori, D.C. / Tomaras, G. / Bonsignori, M. / Santra, S. / Kepler, T.B. / Alam, S.M. / Moody, M.A. / Liao, H.-X. / Haynes, B.F.
CitationJournal: Immunity / Year: 2014
Title: Antibody Light-Chain-Restricted Recognition of the Site of Immune Pressure in the RV144 HIV-1 Vaccine Trial Is Phylogenetically Conserved.
Authors: Wiehe, K. / Easterhoff, D. / Luo, K. / Nicely, N.I. / Bradley, T. / Jaeger, F.H. / Dennison, S.M. / Zhang, R. / Lloyd, K.E. / Stolarchuk, C. / Parks, R. / Sutherland, L.L. / Scearce, R.M. / ...Authors: Wiehe, K. / Easterhoff, D. / Luo, K. / Nicely, N.I. / Bradley, T. / Jaeger, F.H. / Dennison, S.M. / Zhang, R. / Lloyd, K.E. / Stolarchuk, C. / Parks, R. / Sutherland, L.L. / Scearce, R.M. / Morris, L. / Kaewkungwal, J. / Nitayaphan, S. / Pitisuttithum, P. / Rerks-Ngarm, S. / Sinangil, F. / Phogat, S. / Michael, N.L. / Kim, J.H. / Kelsoe, G. / Montefiori, D.C. / Tomaras, G.D. / Bonsignori, M. / Santra, S. / Kepler, T.B. / Alam, S.M. / Moody, M.A. / Liao, H.X. / Haynes, B.F.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CH59UA Fab fragment of heavy chain
L: Inferred unmutated ancestor (UA) of anti-HIV antibody CH59
A: CH59UA Fab fragment of heavy chain
B: Inferred unmutated ancestor (UA) of anti-HIV antibody CH59
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82412
Polymers93,6744
Non-polymers1,1508
Water3,621201
1
H: CH59UA Fab fragment of heavy chain
L: Inferred unmutated ancestor (UA) of anti-HIV antibody CH59
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2185
Polymers46,8372
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-21 kcal/mol
Surface area20290 Å2
MethodPISA
2
A: CH59UA Fab fragment of heavy chain
B: Inferred unmutated ancestor (UA) of anti-HIV antibody CH59
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6067
Polymers46,8372
Non-polymers7695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-17 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.332, 70.803, 107.314
Angle α, β, γ (deg.)90.00, 96.84, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a heterodimer consisting of one H chain and one L chain or one A chain and one B chain.

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody CH59UA Fab fragment of heavy chain


Mass: 23958.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#2: Antibody Inferred unmutated ancestor (UA) of anti-HIV antibody CH59


Mass: 22878.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 209 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: A drop of 0.3 ul protein plus 0.3 ul reservoir, over the 60 ul reservoir which was 0.05 M CaCl2 dihydrate, 0.1 M MES monohydrate pH 6.0, 45% PEG 200., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2012
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25.8 Å / Num. all: 44705 / Num. obs: 44571 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Rsym value: 0.09 / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Mature unliganded CH59 Fab

Resolution: 2.4→25.8 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1887 4.49 %Random
Rwork0.182 ---
all0.1841 44958 --
obs0.1841 41986 93.39 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.548 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4684 Å20 Å24.8318 Å2
2---1.9898 Å20 Å2
3---1.5214 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6361 0 72 201 6634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066604
X-RAY DIFFRACTIONf_angle_d1.0688975
X-RAY DIFFRACTIONf_dihedral_angle_d13.7582385
X-RAY DIFFRACTIONf_chiral_restr0.069995
X-RAY DIFFRACTIONf_plane_restr0.0051145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3953-2.460.27071250.21172718X-RAY DIFFRACTION83
2.46-2.53240.26631420.19442920X-RAY DIFFRACTION89
2.5324-2.6140.24541400.18842887X-RAY DIFFRACTION88
2.614-2.70740.25121360.18372891X-RAY DIFFRACTION89
2.7074-2.81560.22391380.19282962X-RAY DIFFRACTION89
2.8156-2.94360.26091440.19342920X-RAY DIFFRACTION90
2.9436-3.09860.26181410.20633026X-RAY DIFFRACTION92
3.0986-3.29230.2621490.20333231X-RAY DIFFRACTION98
3.2923-3.54590.24671540.20123284X-RAY DIFFRACTION100
3.5459-3.90170.23411550.18363295X-RAY DIFFRACTION100
3.9017-4.46380.18481510.14883292X-RAY DIFFRACTION99
4.4638-5.61440.191530.1473291X-RAY DIFFRACTION99
5.6144-25.87060.21861590.19093382X-RAY DIFFRACTION99
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)
14.7507-2.15332.58554.1151-1.54423.799-0.0627-0.12510.43090.20850.12330.3283-0.5738-0.10060.09250.2893-0.0250.0780.0625-0.01930.258263.40396.3637362.65
21.50140.3854-0.84842.08480.2311.84260.1370.05090.07240.07950.01820.0349-0.21910.0659-0.1160.1350.00930.00250.0499-0.01030.059170.7614-2.6017356.4135
32.566-1.7584-1.86595.34870.1152.23330.18430.31190.1668-0.04080.14730.4028-0.0743-0.0971-0.29430.16370.00490.01520.12780.03940.1562.2432-1.7967358.9296
47.00746.3607-1.09997.7487-3.46835.2731-0.13020.5367-0.5096-0.0110.2518-1.24970.51431.692-0.04710.22460.0322-0.02690.5043-0.08630.221278.5851-17.5204357.5974
51.9704-1.7359-0.64744.04031.16943.3899-0.1747-0.27950.11310.32350.25940.1794-0.3246-0.0946-0.02320.21680.03280.10560.09740.020.095363.1523-2.7002364.9197
61.6357-0.01270.79315.67060.03241.74310.1931-0.04490.1229-0.1529-0.08040.2550.2707-0.0872-0.07310.28020.00640.09050.09110.01320.476630.42040.1629373.6912
73.86581.8934-2.40391.9204-3.51056.9770.56860.37220.77970.43930.05360.0733-0.62850.0983-0.61960.3819-0.00690.08720.13610.06720.448935.29262.3212371.1259
80.58830.23390.00523.80182.08121.1655-0.1083-0.2491-0.1070.56420.0761-0.91320.53650.46770.11220.35140.0786-0.02620.2290.07330.634137.1993-1.5719380.4706
92.30450.93920.11928.7717-0.07663.3135-0.0915-0.1001-0.13330.4535-0.1916-0.16820.1656-0.09730.22980.32150.05470.06450.15490.0180.49531.84920.6651378.6385
105.85542.47684.6465.9761-1.31485.86920.266-0.6083-0.32840.2552-0.23271.6781-0.7546-1.04080.06320.37090.00860.16350.435-0.23570.872721.39270.4827378.6442
115.72712.4371-1.25245.2437-1.52555.67530.3050.55290.2862-0.22530.1240.6566-0.6493-0.3931-0.47010.2750.0669-0.00470.20740.06550.180554.5428-21.1039358.103
122.3680.5177-2.39840.9736-0.80236.3186-0.16970.0659-0.32460.01870.10730.03090.3936-0.41420.02280.2331-0.0234-0.00860.1140.02990.16460.8125-27.9057360.1476
132.3172-0.6532-0.29313.7979-0.99740.644-0.0825-0.29750.00020.27260.19280.02510.3120.03910.0060.2080.0076-0.00210.14420.07150.074367.0434-19.2831365.3648
140.87841.37270.92212.15651.25778.17530.2195-0.206-0.4706-0.0116-0.1323-0.31570.73210.2411-0.03750.22460.09310.02610.19540.08870.198468.7918-28.1548364.737
152.03760.355-1.16212.3514-1.62492.91490.1589-0.14780.06480.11310.08770.11470.0044-0.1399-0.21620.16360.0058-0.01530.08290.01240.08861.8179-20.5023362.6576
163.6565-2.66340.62233.3061-0.53911.16450.0096-0.0093-0.0054-0.0375-0.1220.5341-0.2113-0.15390.00980.20270.0053-0.040.08660.02690.283434.0009-11.8202371.3968
175.4755-4.97541.66779.3071-3.51023.9372-0.0813-0.0440.1214-0.2651-0.03830.1419-0.1925-0.1983-0.05960.2630.00880.01630.08450.05690.305337.7907-13.858368.604
183.85974.1732-0.84338.04524.14637.42620.1134-0.051-0.6168-0.7223-0.8135-0.94031.25070.27140.52561.00030.1343-0.1610.44560.18550.642733.6157-13.6232354.2487
198.4486-0.4043.89245.41263.40034.1781-0.26020.14170.67860.638-0.0821-0.2361-1.13380.54230.36010.4299-0.04670.08130.0938-0.01690.386244.1788-10.5629372.6998
204.8067-1.50380.51145.9653-1.0932.06840.070.46330.1431-0.5394-0.23120.4483-0.3066-0.18860.07780.40120.0856-0.05690.151-0.02240.32332.7742-13.5075364.4773
213.1136-0.5178-1.63640.9797-1.09033.4355-0.10150.41950.5569-0.36820.22690.0765-0.3873-0.1571-0.16480.1330.0130.0570.22140.07610.178280.5831-0.5652324.0652
222.2189-0.69190.82470.48760.54492.67340.09640.37730.3831-0.09860.15820.0693-0.197-0.2199-0.04410.09260.05070.10.21980.09570.103369.4217-4.6344328.5685
230.9145-1.2085-0.56253.98640.03974.2410.18360.13310.1306-0.2238-0.0917-0.2911-0.03290.24170.03040.08360.0033-0.02790.10910.06810.065581.2377-9.9746332.6376
243.6632-0.06040.26331.7574-0.17151.78920.02370.03450.38980.09110.0658-0.0188-0.2663-0.03510.02640.08690.0168-0.00130.10710.03060.075972.3416-2.4231336.4726
253.65631.2755-2.96415.4248-1.44712.48820.2339-0.15130.43850.0461-0.0524-0.3531-0.1306-0.0469-0.17870.12810.02560.00010.11640.00850.154682.792-4.2995331.0138
266.99660.30362.46684.78032.47046.9235-0.0049-0.1397-0.1023-0.1324-0.05910.31960.2652-0.971-0.03660.1771-0.0178-0.02920.2739-0.00690.058568.5837-19.2192333.5487
274.04340.5893-1.93610.5237-1.41723.8766-0.12720.34840.3564-0.40420.1483-0.3366-0.3149-0.06-0.09370.14220.04050.10160.1608-0.03020.306887.1497-2.7247324.3955
285.5905-2.0817-2.1713.8372-0.47362.55910.029-0.0293-0.2201-0.2389-0.22530.35230.3091-0.08780.19070.1712-0.027-0.01660.2238-0.0740.3077111.3376-7.5651315.335
294.4539-2.2627-1.78926.20691.7873.50240.00050.3106-0.1671-0.287-0.4170.01180.43190.0850.29590.19810.03950.0640.3129-0.03210.3082112.9462-6.119314.3221
304.511-4.49333.56635.0201-2.57444.5744-0.21820.40780.4416-0.5868-0.4863-1.83060.27851.08960.49620.26860.04750.09890.49320.11580.5558122.6425-4.812312.4069
315.0812-4.6766-3.73645.62064.84626.06410.0976-0.56941.18890.26390.3518-0.5492-1.12590.6557-0.53290.37160.027-0.01570.2294-0.11050.305389.1422-21.0501340.8829
323.6517-0.6114-2.90360.92051.64385.9989-0.0684-0.126-0.20590.28260.291-0.11190.64320.4402-0.22160.17230.0194-0.05880.1529-0.01240.149587.64-31.5096334.1317
331.39270.1137-0.31072.48490.33192.5773-0.02010.2085-0.0394-0.110.01360.05820.3306-0.09660.05160.08770.0056-0.00190.1384-0.0460.013677.8806-24.3454331.5516
342.98190.371.48362.4131.65625.6249-0.02230.1885-0.34110.0701-0.1010.27650.5622-0.1484-0.21910.2323-0.07880.03620.1652-0.06550.153777.5915-32.7415332.7749
351.5431-0.0339-1.19581.4810.93992.58290.10970.1951-0.01910.3031-0.085-0.1030.0888-0.35590.03010.16460.0012-0.02440.154-0.02090.080482.4082-24.4645332.0257
363.2599-1.6166-1.77955.80875.26276.32650.12120.19070.1028-0.21370.5424-0.5143-0.24680.5286-0.18480.1416-0.0089-0.04130.17920.01440.0987.71-24.0767329.0085
376.80994.40722.09645.92442.14383.4486-0.1330.34240.121-0.1074-0.147-0.0804-0.22690.42650.06450.127-0.0133-0.10890.361-0.01770.3546115.2386-16.1749322.4417
383.39212.06090.22152.5696-0.16291.45030.1254-0.21970.23980.392-0.48710.13910.07140.04470.15390.136-0.1220.01680.3264-0.09520.2247110.2225-20.8566327.4657
397.63111.72553.94264.96522.49477.13010.256-0.01290.2862-0.0426-0.1780.2816-0.1635-0.2080.08750.1155-0.08720.01780.2307-0.10220.3237103.2622-18.6786322.4687
402.2103-1.10870.58852.68810.6961.3410.0531-0.30670.18960.1833-0.1133-0.4863-0.25320.2879-0.08120.1795-0.1477-0.08640.46160.00290.2645116.9576-19.6832331.0924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A and resid 3:19 )A3 - 19
2X-RAY DIFFRACTION2( chain A and resid 20:82 )A20 - 82
3X-RAY DIFFRACTION3( chain A and resid 82A:96 )A82A - 96
4X-RAY DIFFRACTION4( chain A and resid 97:100B )A97 - 100B
5X-RAY DIFFRACTION5( chain A and resid 100C:114 )A100C - 114
6X-RAY DIFFRACTION6( chain A and resid 115:139 )A115 - 139
7X-RAY DIFFRACTION7( chain A and resid 140:145 )A140 - 145
8X-RAY DIFFRACTION8( chain A and resid 146:170 )A146 - 170
9X-RAY DIFFRACTION9( chain A and resid 171:208 )A171 - 208
10X-RAY DIFFRACTION10( chain A and resid 209:213 )A209 - 213
11X-RAY DIFFRACTION11( chain B and resid 1:12 )B1 - 12
12X-RAY DIFFRACTION12( chain B and resid 13:33 )B13 - 33
13X-RAY DIFFRACTION13( chain B and resid 34:52 )B34 - 52
14X-RAY DIFFRACTION14( chain B and resid 53:70 )B53 - 70
15X-RAY DIFFRACTION15( chain B and resid 71:104 )B71 - 104
16X-RAY DIFFRACTION16( chain B and resid 105:128 )B105 - 128
17X-RAY DIFFRACTION17( chain B and resid 129:149 )B129 - 149
18X-RAY DIFFRACTION18( chain B and resid 150:158 )B150 - 158
19X-RAY DIFFRACTION19( chain B and resid 159:168 )B159 - 168
20X-RAY DIFFRACTION20( chain B and resid 169:208 )B169 - 208
21X-RAY DIFFRACTION21( chain H and resid 3:15 )H3 - 15
22X-RAY DIFFRACTION22( chain H and resid 16:33 )H16 - 33
23X-RAY DIFFRACTION23( chain H and resid 34:51 )H34 - 51
24X-RAY DIFFRACTION24( chain H and resid 52:81 )H52 - 81
25X-RAY DIFFRACTION25( chain H and resid 82:95 )H82 - 95
26X-RAY DIFFRACTION26( chain H and resid 96:102 )H96 - 102
27X-RAY DIFFRACTION27( chain H and resid 103:116 )H103 - 116
28X-RAY DIFFRACTION28( chain H and resid 117:169 )H117 - 169
29X-RAY DIFFRACTION29( chain H and resid 170:207 )H170 - 207
30X-RAY DIFFRACTION30( chain H and resid 208:213 )H208 - 213
31X-RAY DIFFRACTION31( chain L and resid 1:7 )L1 - 7
32X-RAY DIFFRACTION32( chain L and resid 8:30 )L8 - 30
33X-RAY DIFFRACTION33( chain L and resid 31:52 )L31 - 52
34X-RAY DIFFRACTION34( chain L and resid 53:74 )L53 - 74
35X-RAY DIFFRACTION35( chain L and resid 75:95B )L75 - 448
36X-RAY DIFFRACTION36( chain L and resid 96:107 )L96 - 107
37X-RAY DIFFRACTION37( chain L and resid 108:128 )L108 - 128
38X-RAY DIFFRACTION38( chain L and resid 129:154 )L129 - 154
39X-RAY DIFFRACTION39( chain L and resid 155:176 )L155 - 176
40X-RAY DIFFRACTION40( chain L and resid 177:208 )L177 - 208

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