1QBK: Karyopherin BETA2

Structure of the karyopherin BETA2-ran gppnhp nuclear transport complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 1 Jun 1999.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,572
Mol. weight: 127.67 kDa
Ligands: MG, GNP
Released: 1 Jun 1999

Explore 1QBK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1QBK contains 73 α-helices and 9 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 67 helices, 0 β-strands

Element	Residues	Length
α-helix	6-9	4
α-helix	12-19	8
α-helix	24-33	10
α-helix	64-69	6
α-helix	70-74	5
α-helix	76-79	4
α-helix	89-95	7
α-helix	98-100	3
α-helix	115-118	4
α-helix	139-141	3
α-helix	153-156	4
α-helix	157-159	3
α-helix	160-164	5
α-helix	177-180	4
α-helix	182-184	3
α-helix	196-199	4
α-helix	200-203	4
α-helix	212-215	4
α-helix	218-221	4
α-helix	234-237	4
α-helix	270-280	11
α-helix	286-289	4
α-helix	315-318	4
α-helix	329-331	3
α-helix	332-334	3
α-helix	341-343	3
α-helix	359-362	4
α-helix	376-382	7
α-helix	395-404	10
α-helix	411-424	14
α-helix	429-432	4
α-helix	436-446	11
α-helix	452-464	13
α-helix	466-470	5
α-helix	474-478	5
α-helix	481-489	9
α-helix	494-511	18
α-helix	516-518	3
α-helix	519-529	11
α-helix	535-552	18
α-helix	553-556	4
α-helix	559-573	15
α-helix	583-596	14
α-helix	602-628	27
α-helix	634-636	3
α-helix	639-655	17
α-helix	660-664	5
α-helix	668-676	9
α-helix	681-697	17
α-helix	699-701	3
α-helix	703-705	3
α-helix	706-715	10
α-helix	719-721	3
α-helix	722-738	17
α-helix	740-746	7
α-helix	748-758	11
α-helix	765-781	17
α-helix	783-786	4
α-helix	787-792	6
α-helix	794-801	8
α-helix	808-823	16
α-helix	825-827	3
α-helix	829-831	3
α-helix	832-839	8
α-helix	847-864	18
α-helix	866-874	9
α-helix	878-887	10

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	1
α-helix	23-31	9
β-strand	46-55	10	1
β-strand	57-65	9	1
β-strand	85-89	5	1
α-helix	102-109	8
β-strand	117-121	5	1
α-helix	133-135	3
α-helix	138-141	4
β-strand	145-148	4	1
β-strand	150	1	2
β-strand	155	1	2
α-helix	159-168	10
β-strand	176	1	1
α-helix	180-181	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Karyopherin BETA2	B	protein	890	Homo sapiens	Q92973 (AlphaFold model)
RAN	C	protein	216	Homo sapiens	P62826 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1QBK_1 KARYOPHERIN BETA2 (chains B)
MEYEWKPDEQGLQQILQLLKESQSPDTTIQRTVQQKLEQLNQYPDFNNYLIFVLTKLKSE
DEPTRSLSGLILKNNVKAHFQNFPNGVTDFIKSECLNNIGDSSPLIRATVGILITTIASK
GELQNWPDLLPKLCSLLDSEDYNTCEGAFGALQKICEDSAEILDSDVLDRPLNIMIPKFL
QFFKHSSPKIRSHAVACVNQFIISRTQALMLHIDSFTENLFALAGDEEPEVRKNVCRALV
MLLEVRMDRLLPHMHNIVEYMLQRTQDQDENVALEACEFWLTLAEQPICKDVLVRHLPKL
IPVLVNGMKYSDIDIILLKGDVEEDETIPDSEQDIRPRFHRSRTVAQQHDEDGIEEEDDD
DDEIDDDDTISDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILV
LGAIAEGCMQGMIPYLPELIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKP
LMTELLKRILDSNKRVQEAACSAFATLEEEACTELVPYLAYILDTLVFAFSKYQHKNLLI
LYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDEDKDLFPLLECLSSVATALQSG
FLPYCEPVYQRCVNLVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLLSGLAEGLGGNIE
QLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPE
FISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGY
VCPQEVAPMLQQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVA
SWINPKDDLRDMFCKILHGFKNQVGDENWRRFSDQFPLPLKERLAAFYGV

Sequence of entity 2 (C), FASTA

>1QBK_2 RAN (chains C)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Primary citation

Structure of the nuclear transport complex karyopherin-beta2-Ran x GppNHp. Chook, Y.M., Blobel, G. Nature (1999) 399:230-237. DOI 10.1038/20375 · PubMed

Other PDB entries of the same protein (UniProt Q92973 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FDD 2.3 Å, Crystal structure of KAP beta2-PY-NLS
2Z5K 2.6 Å, Complex of Transportin 1 with TAP NLS
4OO6 2.7 Å, Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma…
7CYL 2.7 Å, Crystal structure of Karyopherin-beta2 in complex with FUS PY-NLS(P525L)
5YVI 2.9 Å, Crystal structure of Karyopherin beta2 in complex with FUS(456-526)
2QMR 3.0 Å, Karyopherin beta2/transportin
2Z5M 3.0 Å, Complex of Transportin 1 with TAP NLS, crystal form 2
4FQ3 3.0 Å, Crystal structure of transportin/FUS-NLS
5TQC 3.0 Å, Crystal structure of transport factor karyopherin-beta 2 in complex with the PY-NLS of…
2H4M 3.05 Å, Karyopherin Beta2/Transportin-M9NLS
4JLQ 3.05 Å, Crystal structure of human Karyopherin-beta2 bound to the PY-NLS of Saccharomyces…
5J3V 3.05 Å, Crystal structure of human Karyopherin-beta2 bound to the histone H3 tail

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