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- PDB-4rir: Structural Analysis of the Unmutated Ancestor of the HIV-1 Envelo... -

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Basic information

Entry
Database: PDB / ID: 4rir
TitleStructural Analysis of the Unmutated Ancestor of the HIV-1 Envelope V2 Region Antibody CH58 Isolated From an RV144 HIV-1 Vaccine Efficacy Trial Vaccinee and Associated with Decreased Transmission Risk
Components
  • CH58-UA Fab heavy chain
  • CH58-UA Fab light chain
KeywordsIMMUNE SYSTEM / antibody / IgG fold / HIV-1 gp120 V2 region
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNicely, N.I. / Wiehe, K. / Kepler, T.B. / Jaeger, F.H. / Dennison, S.M. / Liao, H.-X. / Alam, S.M. / Hwang, K.-K. / Bonsignori, M. / Rerks-Ngarm, S. ...Nicely, N.I. / Wiehe, K. / Kepler, T.B. / Jaeger, F.H. / Dennison, S.M. / Liao, H.-X. / Alam, S.M. / Hwang, K.-K. / Bonsignori, M. / Rerks-Ngarm, S. / Nitayaphan, S. / Pitisuttithum, P. / Kaewkungwal, J. / Robb, M.L. / O'Connell, R.J. / Michael, N.L. / Kim, J.H. / Haynes, B.F.
CitationJournal: EBioMedicine / Year: 2015
Title: Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 vaccine efficacy trial vaccinee.
Authors: Nicely, N.I. / Wiehe, K. / Kepler, T.B. / Jaeger, F.H. / Dennison, S.M. / Rerks-Ngarm, S. / Nitayaphan, S. / Pitisuttithum, P. / Kaewkungwal, J. / Robb, M.L. / O'Connell, R.J. / Michael, N.L. ...Authors: Nicely, N.I. / Wiehe, K. / Kepler, T.B. / Jaeger, F.H. / Dennison, S.M. / Rerks-Ngarm, S. / Nitayaphan, S. / Pitisuttithum, P. / Kaewkungwal, J. / Robb, M.L. / O'Connell, R.J. / Michael, N.L. / Kim, J.H. / Liao, H.X. / Munir Alam, S. / Hwang, K.K. / Bonsignori, M. / Haynes, B.F.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CH58-UA Fab heavy chain
L: CH58-UA Fab light chain
A: CH58-UA Fab heavy chain
B: CH58-UA Fab light chain


Theoretical massNumber of molelcules
Total (without water)96,2414
Polymers96,2414
Non-polymers00
Water2,018112
1
H: CH58-UA Fab heavy chain
L: CH58-UA Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,1202
Polymers48,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-22 kcal/mol
Surface area20030 Å2
MethodPISA
2
A: CH58-UA Fab heavy chain
B: CH58-UA Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,1202
Polymers48,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.723, 103.707, 101.188
Angle α, β, γ (deg.)90.00, 100.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CH58-UA Fab heavy chain


Mass: 24949.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expi293 / Production host: Homo sapiens (human)
#2: Antibody CH58-UA Fab light chain


Mass: 23170.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expi293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: A drop composed of 0.3 ul protein and 0.3 ul 25 mM MES, pH 6.0, 1.5% PEG 3350 over a reservoir of 50 ul 24% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2012
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 34886 / Num. obs: 33979 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25.915 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 1870 5.5 %randomized selection
Rwork0.2204 ---
obs0.2242 33979 89.52 %-
all-34886 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.295 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6455 Å2-0 Å2-1.455 Å2
2---4.2786 Å2-0 Å2
3----1.3669 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 0 112 6690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056762
X-RAY DIFFRACTIONf_angle_d0.9439212
X-RAY DIFFRACTIONf_dihedral_angle_d13.582390
X-RAY DIFFRACTIONf_chiral_restr0.0641018
X-RAY DIFFRACTIONf_plane_restr0.0051170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56420.42991160.30792045X-RAY DIFFRACTION74
2.5642-2.63960.34391210.30122197X-RAY DIFFRACTION81
2.6396-2.72470.40471410.30282264X-RAY DIFFRACTION83
2.7247-2.8220.38111470.28272275X-RAY DIFFRACTION83
2.822-2.93480.34791340.25712340X-RAY DIFFRACTION85
2.9348-3.06820.34581420.24782441X-RAY DIFFRACTION89
3.0682-3.22960.30791430.2432544X-RAY DIFFRACTION93
3.2296-3.43160.31011530.24222683X-RAY DIFFRACTION97
3.4316-3.69580.30071560.23622641X-RAY DIFFRACTION97
3.6958-4.06650.24951490.20322629X-RAY DIFFRACTION95
4.0665-4.65190.2231590.14412666X-RAY DIFFRACTION96
4.6519-5.84980.2221520.16992677X-RAY DIFFRACTION96
5.8498-25.91620.20611570.18222707X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3270.1635-0.26450.6708-0.36310.7463-0.2435-0.0428-0.1231-0.07280.0263-0.0730.26970.1001-0.07410.63480.03130.08660.03520.09120.060360.23729.473386.4469
20.94960.27240.11460.9220.09840.99590.0224-0.0933-0.0363-0.1294-0.0848-0.1786-0.04450.17840.11850.21370.01020.18650.05280.11070.052263.10336.827193.8385
30.8153-0.403-0.232.51961.06451.2739-0.0808-0.08520.09280.10310.1297-0.42380.08060.1591-0.29540.4190.15340.07950.0654-0.00590.225568.086934.757788.7334
42.3845-1.27520.03221.5313-0.17530.02980.09570.11920.0622-0.2067-0.1959-0.17140.22850.24680.15850.38350.22440.20490.34060.28020.383470.602326.604693.1497
50.78740.372-0.54862.2226-0.28131.2534-0.1874-0.01810.0242-0.1230.02540.079-0.05430.0606-0.12140.33940.07750.038-0.00480.1170.070656.053940.301491.4101
60.65160.0278-0.2352.5154-0.14051.2462-0.0615-0.0834-0.1211-0.1409-0.0682-0.08260.24250.11-0.01040.31980.14670.06520.04480.04590.053555.921234.285492.1062
75.48851.18962.70536.1233-0.94125.01470.11130.6640.8271-0.595-0.1995-0.5109-1.18020.57210.07430.3310.04380.05540.13020.13730.261367.6197.9742109.5376
80.84170.97110.74012.34320.55383.15720.0601-0.05820.02450.0292-0.08450.0425-0.1213-0.0829-0.00650.1806-0.1052-0.00220.07590.0130.042159.072810.4516123.9456
90.14250.04130.01340.6525-0.0530.29990.1082-0.0178-0.0668-0.0080.07960.09420.0371-0.01970.14350.1922-0.1218-0.0629-0.1130.0410.003453.88367.372122.2301
102.3357-0.8782-0.62053.4693-0.65123.0388-0.0711-0.3318-0.20370.3530.0890.10250.6020.0702-0.02430.2004-0.0159-0.08030.17080.1030.111959.43721.7197127.7847
111.79780.04721.02651.692-0.68322.4141-0.0436-0.1185-0.07470.03340.14560.1943-0.0502-0.0922-0.0170.07450.04610.00770.15840.0815-0.038446.902342.0986110.5972
121.3357-0.42230.50361.5122-0.94473.10870.11860.0208-0.0312-0.11710.11150.2359-0.0342-0.0778-0.09840.19310.0290.03190.07420.06050.030651.057643.3189100.4379
131.5460.22840.50631.5687-0.51941.42370.04240.07530.13580.12270.11890.1611-0.0934-0.1940.03490.21490.1291-0.13970.11580.09930.084943.261648.6461100.5622
142.0888-0.2277-0.73321.89020.11612.71470.0224-0.0970.0468-0.04040.01620.2978-0.0429-0.23050.01170.06010.0068-0.04950.09490.00140.103948.242441.0256102.1058
150.1185-0.16580.22430.4392-0.58820.77960.0464-0.0443-0.0862-0.07870.1340.18650.073-0.236-0.11960.0439-0.0375-0.07660.18850.03390.073945.72528.4814119.5508
166.99321.5087-4.33536.48362.90935.08820.2338-0.4001-0.92090.16220.0331-0.40830.73420.3056-0.240.3299-0.0566-0.16070.15260.05130.229168.745511.3896130.3483
171.138-0.69940.55241.4846-0.60210.97940.09330.0950.0198-0.0843-0.00640.10970.0302-0.0436-0.0520.15620.0155-0.14450.0220.05950.058255.604523.4732122.5981
183.3799-1.7658-0.17377.97042.54641.74510.01850.01060.3779-0.3734-0.1453-0.2097-0.5215-0.31030.15510.46310.02750.10980.1278-0.06810.312766.081232.1487126.1634
192.9768-3.00691.20374.1867-0.85422.69010.1105-0.0843-0.4219-0.09460.17760.5554-0.0817-0.2261-0.11620.24160.07940.11980.04490.01380.129451.14221.5386117.4508
200.93530.53540.33610.34430.43051.6856-0.053-0.04550.10720.01630.1343-0.0282-0.0765-0.05880.22090.1623-0.0646-0.2089-0.0031-0.06320.032462.119226.7261130.6668
211.4628-0.54350.94177.37331.02952.07560.03620.0914-0.0433-0.5359-0.03410.1842-0.10970.0470.01350.1428-0.005-0.11960.02270.0510.145223.7981-2.6867133.2961
221.7395-0.4274-0.42290.19060.05620.619-0.0482-0.13360.18820.0445-0.04460.0423-0.0416-0.0437-0.0240.02930.0497-0.05010.1226-0.1380.158116.96175.3362148.9298
230.04970.1656-0.04031.56010.13860.1005-0.01670.00540.1216-0.2711-0.01190.1032-0.09310.06880.04640.0574-0.0202-0.01620.0787-0.02640.060921.5919-9.9718137.4127
241.31930.42060.12190.7211-0.02150.58170.1263-0.18670.0010.0087-0.05140.14990.1371-0.18990.01720.0252-0.0761-0.0390.05570.00570.042818.575-14.1311145.9648
253.0742-1.0946-0.35691.6875-0.27361.47390.0175-0.0501-0.05470.00190.03810.0333-0.0402-0.0618-0.0332-0.00940.04290.00240.02940.07730.117512.7373-7.3847138.8542
260.75060.12260.20550.1721-0.12130.2610.0506-0.09990.0539-0.0271-0.00030.00370.03580.0317-0.0154-0.1372-0.0217-0.0784-0.1569-0.09530.05224.1401-10.4171141.0859
272.1452-1.3399-0.21821.5583-0.76791.67850.0555-0.0833-0.3272-0.0164-0.1074-0.01180.04240.0001-0.17850.0175-0.001-0.00030.05150.04310.066843.233415.1537166.9881
280.9766-0.27840.92760.3716-0.49771.4629-0.01560.10350.1007-0.03850.04630.0924-0.005-0.0418-0.0062-0.0184-0.06510.01890.01340.06640.079537.223115.1267160.7765
290.9967-0.08050.13841.1358-0.08460.432-0.0375-0.00580.09380.0492-0.0277-0.2487-0.10640.0610.0168-0.0424-0.0025-0.10940.02140.0350.036846.912817.691162.2022
305.5955-3.3658-0.99117.83340.24921.0879-0.2361-0.4760.44640.77920.1093-0.5668-0.33830.15790.07670.1583-0.07110.00980.0766-0.03310.094448.143121.9763171.6807
310.3632-0.0731-0.01270.37870.10560.2509-0.0067-0.0179-0.0831-0.04210.008-0.0546-0.02350.082-0.0368-0.00860.0350.0015-0.035-0.03920.056239.5385-18.6346144.6515
321.76470.4758-0.05271.2347-0.33471.87580.08350.1174-0.1422-0.065-0.0754-0.10550.1738-0.01750.07040.0477-0.00550.03890.0421-0.04460.083442.8959-23.7526139.0351
333.03190.2767-0.10831.4470.20661.19550.05920.01060.16650.03220.0789-0.12450.04710.147-0.07230.07310.03960.01620.04540.01380.066539.0973-15.5288142.0866
340.024-0.0364-0.00290.08970.07310.15260.0405-0.02920.0314-0.02230.0432-0.0385-0.01530.05730.1146-0.0316-0.04280.04410.0429-0.074-0.01845.7074-10.3557147.4648
350.43050.0832-0.14771.66310.64561.99240.0066-0.0676-0.08280.099-0.06810.0824-0.0358-0.1103-0.02220.0582-0.00550.01660.00560.0270.043945.62384.031166.8806
363.92431.4863-2.3433.5514-0.5811.43020.03470.2164-0.2006-0.5289-0.00220.10120.49320.0052-0.08150.2138-0.0269-0.08450.06310.04790.182840.6589-8.2065173.219
372.18960.18130.10590.84210.20861.7772-0.0460.29170.0768-0.0420.00690.0802-0.0757-0.275-0.00290.0665-0.0035-0.1180.0429-0.0140.072944.78662.8987158.0757
380.8361-0.1619-0.22061.0863-1.02241.5894-0.0849-0.1028-0.07740.1850.09430.12840.0542-0.04740.08250.17360.0180.08940.06480.08490.006842.0946-1.2583176.5478
397.14851.66150.52418.2869-2.78281.1062-0.07760.0208-0.5684-0.0698-0.00850.14660.9031-0.14720.07550.1279-0.065-0.00160.05140.02850.15252.8019-8.7314161.2074
402.1489-1.23490.41395.2557-2.77628.1196-0.2131-0.28350.09220.40530.0993-0.041-0.77310.21870.13550.29860.08830.02790.21180.05430.144549.76341.8249178.2399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:36)
2X-RAY DIFFRACTION2(chain A and resid 37:58)
3X-RAY DIFFRACTION3(chain A and resid 59:78)
4X-RAY DIFFRACTION4(chain A and resid 79:83)
5X-RAY DIFFRACTION5(chain A and resid 84:100D)
6X-RAY DIFFRACTION6(chain A and resid 100E:112)
7X-RAY DIFFRACTION7(chain A and resid 113:119)
8X-RAY DIFFRACTION8(chain A and resid 120:147)
9X-RAY DIFFRACTION9(chain A and resid 148:204)
10X-RAY DIFFRACTION10(chain A and resid 205:213)
11X-RAY DIFFRACTION11(chain B and resid 1:24)
12X-RAY DIFFRACTION12(chain B and resid 25:46)
13X-RAY DIFFRACTION13(chain B and resid 47:72)
14X-RAY DIFFRACTION14(chain B and resid 73:98)
15X-RAY DIFFRACTION15(chain B and resid 99:119)
16X-RAY DIFFRACTION16(chain B and resid 120:126)
17X-RAY DIFFRACTION17(chain B and resid 127:148)
18X-RAY DIFFRACTION18(chain B and resid 149:158)
19X-RAY DIFFRACTION19(chain B and resid 159:179)
20X-RAY DIFFRACTION20(chain B and resid 180:210)
21X-RAY DIFFRACTION21(chain H and resid 1:10)
22X-RAY DIFFRACTION22(chain H and resid 11:20)
23X-RAY DIFFRACTION23(chain H and resid 21:42)
24X-RAY DIFFRACTION24(chain H and resid 43:65)
25X-RAY DIFFRACTION25(chain H and resid 66:78)
26X-RAY DIFFRACTION26(chain H and resid 79:113)
27X-RAY DIFFRACTION27(chain H and resid 114:138)
28X-RAY DIFFRACTION28(chain H and resid 139:150)
29X-RAY DIFFRACTION29(chain H and resid 151:206)
30X-RAY DIFFRACTION30(chain H and resid 207:213)
31X-RAY DIFFRACTION31(chain L and resid 1:50)
32X-RAY DIFFRACTION32(chain L and resid 51:75)
33X-RAY DIFFRACTION33(chain L and resid 76:95)
34X-RAY DIFFRACTION34(chain L and resid 96:112)
35X-RAY DIFFRACTION35(chain L and resid 113:148)
36X-RAY DIFFRACTION36(chain L and resid 149:156)
37X-RAY DIFFRACTION37(chain L and resid 157:180)
38X-RAY DIFFRACTION38(chain L and resid 181:196)
39X-RAY DIFFRACTION39(chain L and resid 197:203)
40X-RAY DIFFRACTION40(chain L and resid 204:210)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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