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- PDB-4jam: Crystal structure of broadly neutralizing anti-hiv-1 antibody ch103 -

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Basic information

Entry
Database: PDB / ID: 4jam
TitleCrystal structure of broadly neutralizing anti-hiv-1 antibody ch103
Components(ANTIGEN BINDING FRAGMENT OF ...) x 2
KeywordsIMMUNE SYSTEM / NEUTRALIZATION / VACCINE / HIV-1 / Antibody / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZhou, T. / Moquin, S. / Zheng, A. / Srivatsan, S. / Kwong, P.D.
CitationJournal: Nature / Year: 2013
Title: Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.
Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / ...Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / Hraber, P. / Wiehe, K. / Kelsoe, G. / Yang, G. / Xia, S.M. / Montefiori, D.C. / Parks, R. / Lloyd, K.E. / Scearce, R.M. / Soderberg, K.A. / Cohen, M. / Kamanga, G. / Louder, M.K. / Tran, L.M. / Chen, Y. / Cai, F. / Chen, S. / Moquin, S. / Du, X. / Joyce, M.G. / Srivatsan, S. / Zhang, B. / Zheng, A. / Shaw, G.M. / Hahn, B.H. / Kepler, T.B. / Korber, B.T. / Kwong, P.D. / Mascola, J.R. / Haynes, B.F.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3May 29, 2013Group: Database references
Revision 1.4Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
L: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
A: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
B: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,23533
Polymers92,8624
Non-polymers2,37429
Water13,079726
1
H: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
L: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,56816
Polymers46,4312
Non-polymers1,13714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-103 kcal/mol
Surface area19050 Å2
MethodPISA
2
A: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
B: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,66817
Polymers46,4312
Non-polymers1,23715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-128 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.027, 146.375, 66.322
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103


Mass: 23896.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human)
#2: Antibody ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103


Mass: 22533.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human)

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Non-polymers , 4 types, 755 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 170 mM ammonium sulfate, 25.5 % PEG 4000, 15% Glycerol, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2012 / Details: APS 22ID
RadiationMonochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 97300 / Num. obs: 95840 / % possible obs: 98.4 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.067 / Net I/σ(I): 30
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.53 / % possible all: 90.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9

3se9


Resolution: 1.65→38.185 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4774 5 %Random
Rwork0.1689 ---
obs0.1703 95522 98.03 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→38.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 134 726 7259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076718
X-RAY DIFFRACTIONf_angle_d1.169159
X-RAY DIFFRACTIONf_dihedral_angle_d13.2252359
X-RAY DIFFRACTIONf_chiral_restr0.0671043
X-RAY DIFFRACTIONf_plane_restr0.0061149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6489-1.66770.28551160.25672667X-RAY DIFFRACTION87
1.6677-1.68730.29241340.24922794X-RAY DIFFRACTION91
1.6873-1.70790.28641420.24052933X-RAY DIFFRACTION94
1.7079-1.72950.28511690.2342917X-RAY DIFFRACTION95
1.7295-1.75220.25451740.232964X-RAY DIFFRACTION97
1.7522-1.77630.25871590.22623006X-RAY DIFFRACTION97
1.7763-1.80160.25931510.22153011X-RAY DIFFRACTION98
1.8016-1.82850.2531460.21393001X-RAY DIFFRACTION98
1.8285-1.85710.24511590.20513076X-RAY DIFFRACTION99
1.8571-1.88750.23011660.18833024X-RAY DIFFRACTION98
1.8875-1.92010.2191530.17662992X-RAY DIFFRACTION99
1.9201-1.9550.20611690.17733140X-RAY DIFFRACTION99
1.955-1.99260.18471400.18052996X-RAY DIFFRACTION99
1.9926-2.03330.22431790.17963066X-RAY DIFFRACTION99
2.0333-2.07750.19321780.17863035X-RAY DIFFRACTION99
2.0775-2.12580.21861790.16663044X-RAY DIFFRACTION99
2.1258-2.1790.21071670.17213088X-RAY DIFFRACTION99
2.179-2.23790.21271640.16873035X-RAY DIFFRACTION99
2.2379-2.30370.2281480.16633083X-RAY DIFFRACTION100
2.3037-2.37810.1881700.16413091X-RAY DIFFRACTION100
2.3781-2.4630.21271530.16553066X-RAY DIFFRACTION100
2.463-2.56160.22051640.17283075X-RAY DIFFRACTION100
2.5616-2.67820.17371710.16423085X-RAY DIFFRACTION99
2.6782-2.81930.19011510.15823062X-RAY DIFFRACTION99
2.8193-2.99590.19241790.15983061X-RAY DIFFRACTION100
2.9959-3.22710.16821470.16253092X-RAY DIFFRACTION100
3.2271-3.55170.20861710.15243084X-RAY DIFFRACTION100
3.5517-4.06510.15171580.15143075X-RAY DIFFRACTION100
4.0651-5.11970.15221690.13593091X-RAY DIFFRACTION100
5.1197-38.19530.21861480.19173094X-RAY DIFFRACTION98
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)
12.41290.39720.87773.4520.51833.3309-0.11630.15850.0262-0.21520.1156-0.1516-0.21280.13240.01220.1012-0.0540.03720.1159-0.03220.15190.9624-17.362729.2686
23.42640.72530.6182.72190.35314.1940.0533-0.15760.20260.1242-0.0976-0.0195-0.38390.44290.02950.161-0.08570.00090.2111-0.00050.084515.068217.782515.0516
32.97462.0807-0.00913.14120.32611.57240.02830.0574-0.37720.22910.0778-0.43840.08240.0866-0.08980.13630.0468-0.05210.0937-0.04580.219613.778-7.933344.5408
41.4867-0.69141.98252.4276-1.47664.7823-0.05970.03530.00190.06120.0697-0.0766-0.2494-0.1374-0.00710.1657-0.02560.03850.15460.00990.07499.517614.973929.9033
54.42061.28281.90322.67371.17535.63450.2708-0.2037-0.04780.2696-0.1575-0.21480.20360.0147-0.06840.2091-0.0487-0.06350.1240.01190.190511.519648.765867.1485
62.8121-0.17140.89492.49420.82974.7271-0.11130.413-0.0411-0.1408-0.0113-0.013-0.16210.20260.09680.1189-0.06170.03420.17250.01690.06738.244118.911759.8778
71.068-0.1895-0.94421.21250.20493.0589-0.0306-0.0130.02320.0588-0.0431-0.22780.11520.10890.05370.0566-0.0170.00720.12820.05470.18426.70940.544447.2981
82.4039-0.2241.06912.327-0.96833.18950.0925-0.1665-0.0374-0.02570.03580.2002-0.0394-0.268-0.07230.05940.00480.03280.1023-0.00510.121222.603117.194355.664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:113
2X-RAY DIFFRACTION2chain H and resid 114:223
3X-RAY DIFFRACTION3chain L and resid 1:108
4X-RAY DIFFRACTION4chain L and resid 109:215
5X-RAY DIFFRACTION5chain A and resid 1:113
6X-RAY DIFFRACTION6chain A and resid 114:223
7X-RAY DIFFRACTION7chain B and resid 1:108
8X-RAY DIFFRACTION8chain B and resid 109:215

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