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- PDB-3tcl: Crystal Structure of HIV-1 Neutralizing Antibody CH04 -

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Basic information

Entry
Database: PDB / ID: 3tcl
TitleCrystal Structure of HIV-1 Neutralizing Antibody CH04
Components
  • CH04 Heavy Chain Fab
  • CH04 Light Chain Fab
KeywordsIMMUNE SYSTEM / Ig / Immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.906 Å
AuthorsLouder, R.K. / McLellan, J.S. / Pancera, M. / Yang, Y. / Zhang, B. / Bonsignori, M. / 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
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 1.4Oct 30, 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: CH04 Heavy Chain Fab
L: CH04 Light Chain Fab
A: CH04 Heavy Chain Fab
B: CH04 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4816
Polymers98,3434
Non-polymers1382
Water11,223623
1
H: CH04 Heavy Chain Fab
L: CH04 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2413
Polymers49,1722
Non-polymers691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-24 kcal/mol
Surface area20180 Å2
MethodPISA
2
A: CH04 Heavy Chain Fab
B: CH04 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2413
Polymers49,1722
Non-polymers691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-24 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.363, 74.227, 183.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CH04 Heavy Chain Fab


Mass: 25417.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody CH04 Light Chain Fab


Mass: 23754.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo Sapiens (human)
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 3% MPD, 0.1M imidazole, , pH 6.5, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 79061 / Num. obs: 78982 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3 / Num. unique all: 3892 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: dev_755)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DFB and 1QLR

1dfb

1qlr


Resolution: 1.906→39.703 Å / SU ML: 0.58 / σ(F): 0 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 3961 5.02 %Random
Rwork0.1956 ---
all0.1977 79201 --
obs0.1977 78886 99.83 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.066 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8215 Å20 Å2-0 Å2
2--4.4015 Å2-0 Å2
3----7.223 Å2
Refinement stepCycle: LAST / Resolution: 1.906→39.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6795 0 10 623 7428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137062
X-RAY DIFFRACTIONf_angle_d1.3879611
X-RAY DIFFRACTIONf_dihedral_angle_d12.8992544
X-RAY DIFFRACTIONf_chiral_restr0.0931048
X-RAY DIFFRACTIONf_plane_restr0.0071251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9063-1.92960.36211480.26222567X-RAY DIFFRACTION97
1.9296-1.9540.26431430.24982632X-RAY DIFFRACTION100
1.954-1.97970.29161210.23252659X-RAY DIFFRACTION100
1.9797-2.00680.27211350.22362665X-RAY DIFFRACTION100
2.0068-2.03550.28721260.2272637X-RAY DIFFRACTION100
2.0355-2.06590.26871480.2222635X-RAY DIFFRACTION100
2.0659-2.09820.31621580.2332642X-RAY DIFFRACTION100
2.0982-2.13260.33421380.22182662X-RAY DIFFRACTION100
2.1326-2.16930.29081400.2252649X-RAY DIFFRACTION100
2.1693-2.20880.28481460.21442616X-RAY DIFFRACTION100
2.2088-2.25130.26431360.21212679X-RAY DIFFRACTION100
2.2513-2.29720.25561550.20382662X-RAY DIFFRACTION100
2.2972-2.34720.2641360.19822646X-RAY DIFFRACTION100
2.3472-2.40180.26351380.19492662X-RAY DIFFRACTION100
2.4018-2.46180.25181440.22651X-RAY DIFFRACTION100
2.4618-2.52840.27261440.20172671X-RAY DIFFRACTION100
2.5284-2.60270.26841730.19482632X-RAY DIFFRACTION100
2.6027-2.68670.23351310.19762675X-RAY DIFFRACTION100
2.6867-2.78270.26761410.19522686X-RAY DIFFRACTION100
2.7827-2.89410.28431360.20612690X-RAY DIFFRACTION100
2.8941-3.02580.21591230.19892687X-RAY DIFFRACTION100
3.0258-3.18530.25261290.18992724X-RAY DIFFRACTION100
3.1853-3.38470.22491400.17892685X-RAY DIFFRACTION100
3.3847-3.64590.18861510.17972688X-RAY DIFFRACTION100
3.6459-4.01250.20671360.17172731X-RAY DIFFRACTION100
4.0125-4.59240.19151450.16162753X-RAY DIFFRACTION100
4.5924-5.7830.17871490.17752750X-RAY DIFFRACTION100
5.783-39.71160.26461510.22812889X-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)
12.042-0.99271.90863.8604-3.07876.6182-0.0504-0.0983-0.09470.00730.17120.17560.035-0.1392-0.10750.1698-0.02150.02940.17270.00070.1458-30.0206-6.2961-13.3001
24.86873.87031.85075.89550.61462.5461-0.17190.03810.31270.0833-0.1001-0.1767-0.40830.26770.23310.2662-0.0141-0.07620.20450.05910.2479-23.947426.107-25.2513
31.11052.2557-0.33096.7789-1.51582.5324-0.0366-0.1493-0.02070.3283-0.0265-0.1715-0.46990.09070.06230.27220.0195-0.00930.30940.03030.1653-27.6993-0.22157.1372
41.81021.51711.83382.00621.10184.0952-0.2518-1.16740.69160.2605-0.61530.4084-0.7827-1.90110.7360.50370.157-0.10130.8923-0.26570.4265-33.629731.0784-13.0321
53.01131.29942.06663.05132.07996.34850.1693-0.1215-0.10170.1307-0.0766-0.16260.2598-0.118-0.0840.14660.0178-0.01040.15980.0210.166423.168523.5316-59.726
67.4447-3.8626-1.44193.01521.35442.715-0.1614-0.21360.54190.1640.0865-0.1485-0.2378-0.12110.07240.2085-0.0016-0.05850.1974-0.05110.2517-10.375830.8019-68.5945
75.7239-3.05921.41912.2588-0.35421.59630.0095-0.2592-0.14080.21260.01020.10620.1138-0.3402-0.01610.2835-0.0727-0.02150.25940.00960.158518.309325.4181-38.9882
84.4411.3381.13678.20813.48876.9309-0.0342-0.5306-0.24410.3275-0.05220.28750.5547-0.34160.09170.22950.04480.02430.31560.05180.2408-13.301720.5943-55.8526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:109
2X-RAY DIFFRACTION2chain L and resid 110:215
3X-RAY DIFFRACTION3chain H and resid 1:134
4X-RAY DIFFRACTION4chain H and resid 135:237
5X-RAY DIFFRACTION5chain B and resid 1:109
6X-RAY DIFFRACTION6chain B and resid 110:215
7X-RAY DIFFRACTION7chain A and resid 1:134
8X-RAY DIFFRACTION8chain A and resid 135:237

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