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- PDB-3u46: CH04H/CH02L P212121 -

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Basic information

Entry
Database: PDB / ID: 3u46
TitleCH04H/CH02L P212121
Components
  • CH02 Light chain Fab
  • CH04 Heavy chain Fab
KeywordsIMMUNE SYSTEM / IGG / Immunogloblulin / HIV-1 Antibodies / V1V2-Directed
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 Å
AuthorsLouder, R. / Pancera, M. / McLellan, J.S. / Kwong, P.D.
CitationJournal: Nature / Year: 2011
Title: Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, ...Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, Y. / Zhang, B. / Zhou, T. / Zhu, J. / Boyington, J.C. / Chuang, G.Y. / Diwanji, D. / Georgiev, I. / Do Kwon, Y. / Lee, D. / Louder, M.K. / Moquin, S. / Schmidt, S.D. / Yang, Z.Y. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Burton, D.R. / Koff, W.C. / Walker, L.M. / Phogat, S. / Wyatt, R. / Orwenyo, J. / Wang, L.X. / Arthos, J. / Bewley, C.A. / Mascola, J.R. / Nabel, G.J. / Schief, W.R. / Ward, A.B. / Wilson, I.A. / Kwong, P.D.
History
DepositionOct 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CH04 Heavy chain Fab
L: CH02 Light chain Fab
A: CH04 Heavy chain Fab
B: CH02 Light chain Fab


Theoretical massNumber of molelcules
Total (without water)98,4414
Polymers98,4414
Non-polymers00
Water39622
1
H: CH04 Heavy chain Fab
L: CH02 Light chain Fab


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-23 kcal/mol
Surface area20500 Å2
MethodPISA
2
A: CH04 Heavy chain Fab
B: CH02 Light chain Fab


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-24 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.607, 105.539, 163.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Antibody CH04 Heavy chain Fab


Mass: 25546.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CH02 Light chain Fab


Mass: 23674.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 16% PEG 400, 8% PEG 8000, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22893
Reflection shellResolution: 2.9→3 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.906→32.373 Å / SU ML: 0.83 / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 1176 5.15 %
Rwork0.2147 --
obs0.2162 22836 82.38 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.836 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-37.0769 Å2-0 Å2-0 Å2
2---20.4986 Å2-0 Å2
3----16.5783 Å2
Refinement stepCycle: LAST / Resolution: 2.906→32.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 0 22 6784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026936
X-RAY DIFFRACTIONf_angle_d0.5829406
X-RAY DIFFRACTIONf_dihedral_angle_d9.8742474
X-RAY DIFFRACTIONf_chiral_restr0.0381017
X-RAY DIFFRACTIONf_plane_restr0.0031225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9064-3.03860.42981080.36271647X-RAY DIFFRACTION51
3.0386-3.19860.3952900.30462001X-RAY DIFFRACTION61
3.1986-3.39880.31491100.27112305X-RAY DIFFRACTION71
3.3988-3.66090.27051450.25042621X-RAY DIFFRACTION81
3.6609-4.02870.26191680.23223032X-RAY DIFFRACTION93
4.0287-4.61030.23471570.17473305X-RAY DIFFRACTION100
4.6103-5.8030.18791980.1783294X-RAY DIFFRACTION100
5.803-32.37520.21682000.19853455X-RAY DIFFRACTION100
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)
12.2641.33740.48236.17421.28873.9616-0.0018-0.0913-0.32970.11150.0014-0.24980.3461-0.0978-0.01920.1212-0.03130.10110.05210.04010.0727-18.570934.71473.0723
21.28430.3628-0.55150.2512-0.86373.60520.08890.37180.0026-0.83040.0663-0.7721-0.0090.5634-0.08351.0986-0.1420.51140.4693-0.16720.7017-9.729419.0577-26.8495
32.95410.1623-1.672.9910.41772.8171-0.26030.09790.0695-0.3574-0.1022-0.3868-0.35440.18190.3160.4593-0.03560.08960.275-0.00440.3556-14.826954.6042-5.0953
41.56940.2374-1.19721.5827-2.42814.52370.09880.20440.1829-0.84220.2594-0.1205-0.0335-0.26410.14381.2652-0.1930.37380.4537-0.03630.4535-20.773429.7835-33.4647
54.6327-2.5251-0.26867.9926-0.55621.12760.09950.01090.5413-0.0901-0.0618-0.6676-0.46340.04640.00820.61540.1774-0.04290.3325-0.03990.33694.609318.4262-64.8966
63.49051.1246-1.94282.4061-1.05075.87620.2251-0.16140.29351.01-0.02790.682-0.1114-0.5437-0.1330.74680.05430.19620.27180.11440.2912-25.559734.2555-57.1967
75.8183-0.6211-1.53322.47330.58511.39750.1825-0.3083-0.96190.48750.03440.27850.26940.1301-0.20150.85760.1951-0.08310.31670.05640.5676-3.5055-1.2299-60.2756
84.60580.72330.45697.45270.47166.04490.17321.25910.0353-0.66440.45290.7861-0.0099-1.065-0.48720.41280.02770.04950.74060.1260.3284-32.154222.5157-67.2865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:110
2X-RAY DIFFRACTION2chain L and resid 111:214
3X-RAY DIFFRACTION3chain H and resid 1:134
4X-RAY DIFFRACTION4chain H and resid 135:233
5X-RAY DIFFRACTION5chain B and resid 1:110
6X-RAY DIFFRACTION6chain B and resid 111:214
7X-RAY DIFFRACTION7chain A and resid 1:134
8X-RAY DIFFRACTION8chain A and resid 135:233

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